Introduction

Bacterial blight (BB, caused by Xanthomonas citri pv. malvacearum, Xcm) has been historically one of the most devastating cotton (Gossypium spp.) diseases worldwide. The development of BB resistant cultivars in the 1970’s and planting of acid-delinted seed has effectively controlled this disease. However, its resurgence has been noted in the US in recent years due to use of BB susceptible cultivars. Popular transgenic Bollguard (with a single Bt gene) cultivars were resistant to BB (including DP 555BR, DP 444BR, and ST 5599BR), but when the single gene Bt trait was replaced with Bollguard II (with two Bt genes), then the majority of U.S. cotton was planted to cultivars susceptible to BB (Phillips et al. 2017; Wheeler 2018). Seed companies have recently placed a higher emphasis on BB resistant cultivars, and as a result, BB has also declined (Wheeler 2020).

Evolution of Xcm races mirrored the development of cotton cultivars with new genes for resistance until the virulent race 18 evolved. Race 18 of Xcm is commonly found in most of the cotton producing regions of the world (Allen and West 1991; Akello and Hillocks 2002; de Sousa Braga et al. 2016; Hussain 1984; Saeedi Madani et al. 2010; Sampath Kumar et al. 2018; Shelke et al. 2012; Thaxton et al. 2001; Zachowski and Rudolph 1988). In a survey of cotton seed in northern Nigeria, only races 1, 12, 13, and 16 were found (Ajene et al. 2014). Race 19 was identified in Brazil (Ruano and Mohan 1982). Highly virulent strains of Xcm in central Africa in the 1970s and 1980s were identified that represent race 20 (Follin et al. 1988). The potential epidemic of this resurgent disease calls for a clear understanding of the genetic basis in resistance to BB in cotton. Although several reviews can be found in articles of Brinkerhorff (1970) and Innes (1983) and book chapters from Verma (1986) and Hillocks (1992), no review with updated knowledge has been published since then. Since most of these reviews and research papers were published in the 1930s to 1980s, it is difficult to obtain their full papers. It is important to understand the history and current affairs of breeding and genetics for BB resistance for identification of new resistance sources carrying different resistance genes and development of research and breeding strategies. This review is to provide a comprehensive summary on the genetic and molecular basis of BB resistance.

Qualitative genetics

In a series of ground-breaking work in Sudan between the 1930s and the 1950s, Knight transferred BB resistance from Upland (G. hirsutum L.) and diploid G. arboreum L., G. herbaceum L. and G. anamalum Waw. & Peyr. to Egyptian (G. barbadense L.) Sakel in Sudan and identified 10 major resistance genes. These genes include B1, B2, and B7 from Upland, B2, B3 and B10 from G. hirsutum race punctatum, B4 and B6 from G. arboreum, B5 from a perennial G. barbadense, recessive gene b8 from G. anomalum, and B9 from G. herbaceum. Several of these genes were also transferred to commercial Upland cultivars in Sudan. In the US, breeding and genetic studies in BB resistance were focused primarily on Upland cotton between the 1940s and 1960s. The efforts resulted in identification of several major B genes including B7 (designated later by Knight), B12, BIn, BN and BS, and several polygene modifiers or complexes. The following is a detailed summary of these research activities and major results (Table 1).

Table 1 Major B genes and polygene complexes for bacterial blight resistance in cotton
Full size table

B1 and B2

Harland (1932) was perhaps first to study the segregation of BB resistance in cotton using crosses between Egyptian and Sea-Island cotton while working in a British cotton research station in Trinidad (West Indies). He noted that the resistance in F1 was intermediate, while segregation in F2 produced a series of gradations in resistance ranging from more susceptible than the susceptible Egyptian to more resistant than the resistant parent. However, most G. barbadense germplasm lines were susceptible, and the resistance levels in some lines were low. However, ground-breaking work on BB resistance did not begin until after Knight (Knight and Clouston 1939) at a British cotton research station in Sudan published results from a study on the genetic basis of BB resistance in a cross of resistant Upland Uganda B31 with susceptible G. barbadense X 1530 and N.T. 2, both selected from Sudan Sakel. They used artificial inoculation and rated > 25,000 plants in F1, F2, BC1F1, and many families from BC2F1, BC3F1, BC1F2, BC2F2, BC3F2, and BC2F3 using a rating scale of 0 for immunity to 12 for the most susceptible plants, similar to the susceptibility of G. barbadense Sakel (11 was omitted in the rating system). This comprehensive genetic study was similarly employed in his many follow-up studies leading to the identification of 10 resistant B genes. A typical 15R (resistant):1S (susceptible) ratio in F2 and many families in backcrosses were observed; so was a typical 3R:1S ratio in BC1F1 and many families in BC2F1 and BC3F1, and a 1R:1S ratio in backcrossing families from plants selected for backcrossing to the susceptible parent. Thus, two major resistance genes B1 and B2 were identified and assigned gene designations. The two susceptible Sakel lines (G. barbadense) had the highest grade 12 and were assigned the b1b1b2b2 genotype, while the resistant Uganda B31 (G. hirsutum) was assigned the B1B1B2B2 genotype. Both B1 and B2 were dominant, but B1 was weak in its resistance and conferred a grade 10.1 resistance, while B2 was strong in resistance with a grade 6 to 7 resistance. However, B2 itself did not provide adequate protection against BB. The combination of B1 and B2 in either the heterozygous or homozygous condition produced a resistance grade of 5 to 6 in the Sakel background. In addition, they noted a close correlation between leaf and stem resistance (r = 0.50–0.63). As a result of backcrossing, the BB resistance genes were successfully transferred from Upland to Sakel, both separately and in single and two-gene combinations while maintaining the spinning quality (Knight 1944). The two genes were accumulative, but in the Sakel background, the two genes did not give the same level of resistance as in Upland B31, suggesting that a modifier complex was lost during the transfer.

Knight (1947) further showed that B1 was closely linked to (or possibly identical to) a recessive dwarf gene, designated da, which produced a 'dwarf-bunched’ phenotype in conjunction with another duplicate recessive gene db. The B2 gene in Uganda B31 was also detected in crossing with susceptible Upland (Knight and Clouston 1941). A number of other Uplands also possessed B2, such as a Punjab Upland selection “513” (Knight and Clouston 1941), Nigerian Allen selections- Albar 49 and its selection Bar 17/1, Albar 51 and its selection Albar 3 MB (giving BA 195/61), Bar 11/5, Bar 11/7 (Innes 1963a), Mwanza Local selections (59/567) and UKBR61/12 from Tanzania (Innes 1965a, 1969), and certain cultivars from the US (Brinkerhoff 1970). Innes (1963b) first suspected that the superior resistance of the Albar derivatives- Bar 17/1 and BA 195/61, compared with that of Bar 11/5 (with B2B2) and Bar 11/7 (with B2B2B3B3), was attributed to the presence of additional modifier and minor genes in combination with B2. Although the presence of B3 was not ruled out, the effect of B3 can be difficult to detect in the presence of B2. However, Innes (1965a) later suggested that the Albar derivatives carried the major gene B2, and possibly B3, as widely assumed due to the result of introgression from G. hirsutum var. punctatum. Interestingly, several G. barbadense also possessed B2 including a Sea-Island origin BAR 898, B 181, NT14 and RU 4 derived from U 4, and SP 84 R heterozygous for B2, and the resistance in some of the genotypes might have been derived from Upland cotton (Knight 1944; Knight and Hutchinson 1950).

B 3

Knight (1944) discovered that BAR3, a strain of G. hirsutum var. punctatum exhibiting a grade 1–2 resistance (0 = immunity; 12 = full susceptibility) possessed two linked resistance genes, B2 and B3. Gene B3 was a partially dominant gene which conferred a grade 7–8.1 resistance when heterozygous and a grade 4.1–7.1 resistance when homozygous in the G. barbadense Sakel background. B2 and B3 were additive, in that B2b2B3b3 and B2B2B3b3 plants exihibited a resistance grade of about 4, and B2B2B3B3 and B2b2B3B3 showed a grade 3 resistance. B2 and B3 were linked at a recombination frequency of 0.324 (Knight 1944). The B2B3 genotype is common in punctatum, as three other punctatum strains-Gambia Native, Hindi Weed and Darfur Local also possessed B2B3. Through backcrossing and selections, B1, B2, and B3 were transferred to the Sakel background individually or in multi-gene combinations, lending the ability to detect individual or accumulated effects of the three B genes, and to use them in allelic tests with other sources of BB resistance. Upland BAR 7/8 and BAR NT 96 possessed B2 and B3 and were commercialized in Sudan. Many selections from Nigerian Allen also carried B2B3 (Innes 1963b, 1965a, 1969).

B 4

Since complete immunity to BB was found in the two Old World cultivated A genome diploid species G. arboreum and G. herbaceum, genetic studies and transfer of this immunity to New World tetraploid cotton species was undertaken by Knight (1948). Through repeated backcrossing up to BC5, the immune (grade 0) Multani (Sangttineum) strain NT 12/30 (belonging to race bengalense of G. arboreum) with colchicine doubled chromosomes was crossed to susceptible Sakel (G. barbadense). Resistance in the F1 (with a synthesized AAAD genome) ranged from 1 to 5 with an average of 2.6, indicating incomplete dominance for resistance. BC4F2 and BC5F3 from fertility restored heterozygous resistant BC4F1 or BC4F2 (grade 6–9) gave a 3R:1S ratio, and the BC5F1 from backcrossing the heterozygous resistant BC4F1 or BC4F2 to Sakel segregated in a 1R:1S ratio, as expected for a major gene, designated B4. B4 is non-allelic to B1, B2, or B3 but additive to B2 and B3. However, no immune plants were observed, indicating that other resistance genes in the immune diploid parent were lost during the interspecific backcrossing process. In diploid F2 and backcross progenies of a cross between NTI2/30 and a susceptible semi-wild Sudan type (race soudanense of G. arboreum) Nuba Red, Knight (1948) confirmed that the immunity in Multani cotton depends on the major B4 gene, accompanied by a strong complex of minor genes.

B 5

Knight (1950) showed that two forms of BB resistance occurred in G. barbadense: weak resistance as represented by cultivated Sea Island lines BA 1–1, BA 1–5, and BA 1–14 from St Vincent, Montserrat, and Barbados, respectively, with resistance grades of 7–10; and strong resistance as represented by perennial Grenadines White Pollen (BP 1–1) with a resistance grade of 5–7. The F2 derived from the most resistant F1 from crossing the above three resistant Sea Island lines with the susceptible Sakel were all as susceptible as Sakel, and resistance was not recovered, indicating that no major gene was present in the three lines. However, the resistance in Grenadines White Pollen was due to the presence of B5 fortified by minor genes. B5 was found to be variable in expression but, in general, the homozygotes (5–6 grade) expressed stronger resistance than the heterozygotes (6–8 grade). B5 was independent of B1 (8–9 grade), B2 (5–6 grade), B3 (5–6 grade), and B4 (6–7) in crosses between Grenadines White Pollen (possessing B5) and four different Sakel lines, each with one of the other four B genes. B5 was additive in its effects when in combination with these other four B genes, respectively, but non-allelic, as 15R:1S ratios were observed in F2 populations.

B 6

Knight (1953a) initially discovered B6m in plants from a BC2 progeny with a resistance grade 3 (better than other progeny) when he was transferring B4 from Multani strain NTI2/30 (G. arboreum) to Sakel (G. barbadense). However, the progeny was found to be an outcross with an unknown line possessing B2. Further backcrossing of these resistant plants to susceptible Sakel and X1730A produced 1 (B2B6m):1 (B2b6m):2 (b2B6m and b2b6m). To verify B6m was indeed from the G. arboreum parent, the diploid parent with chromosome doubling was again crossed and backcrossed with Sakel. Since B6m did not exact any effect on BB resistance in the absence of other B genes, individual BC2 plants with grade 12 were crossed with a Sakel line BLR 14/16 possessing B2. The individual F1 plants were then crossed with the susceptible Sakel, which gave a ratio of 1 (B2B6m) (3–5 grade):1 (B2b6m) (5–7 grade):2 (b2B6m and b2b6m) (grade 12). B6m increased the resistance of B2 by approximately two grades. B6m in combination with B2 and B3 conferred a resistance closely approaching immunity in the Sudan Sakel background (G. barbadense).

In Sudan, however, Innes (1962) later isolated B6m in the Sakel background alone and showed that the resistance of Sakel with B6m, was similar to that of B2 when inoculated with Xcm by foliar spraying and vein inoculation, suggesting similar mechanisms for the two genes. Saunders and Innes (1963) further showed that B6m was in fact a recessive resistance gene of moderate effect when homozygous (b6b6, 7–9 grade), as the progeny (F2 and F3) of heterozygotes produced a ratio of 1R (b6b6): 3S (B6B6 and B6b6, 10–12 grade). They then simplified the gene symbol to B6, but the resistance allele should be named as b6 due to its recessive nature. B6 was additive in its effects when combined with B2, B3, B4 or B5 but not with B1 or B7. B6 with B2 was the most effective combination, giving 3–6 grades, while B2B2/B2b2 or b6b6 alone gave 6–9 grades. Innes (1969) further showed that the B6 gene was present in Mwanza Local UKBR61/12 and that the high resistance of subsequent selections 59/567 resulted from the interaction of B2 with a gene, or a complex of genes occupying the same locus as or closely linked to B6. The B6-type gene was obtained by steady selection pressure to gradually increase BB resistance over years.

B 7

The American Upland Stoneville 20 cultivar, which was resistant to BB in leaves, stems and bolls, was selected from the susceptible cultivar Stoneville 2A (Simpson and Weindling 1946). This resistance was transferred to other susceptible Upland cultivars in the US through backcrossing, and it became a major resistance source used in many breeding programs across the country (Simpson and Weindling 1946). In 1946, Simpson indicated that the resistance in Stoneville 20 was inherited as a simple recessive character but its full expression required modifying or minor genes. Through crosses between Stoneville 20 and several susceptible Uplands, Blank (1949), in Texas, confirmed that the resistance was inherited as a single recessive gene, when the expected 1R:3S ratio was observed in F2 populations and the progeny of segregating BC1F1 and BC1F2 plants. Green and Brinkerhoff (1956) in Oklahoma confirmed that resistance in Stoneville 20 was indeed controlled by a major recessive gene named b7, but that segregation was obscured by other genes of lesser individual effect. In the US, Stoneville 20 was highly resistant to race 1 but only slightly resistant to race 2. Bird and Hadley (1959), in Texas, further studied four parents including Stoneville 20 and their F1, F2, F3 and backcross progenies and demonstred that the dominance of BB resistance to race 1 and 2 in Stoneville 20 depended on the other parent used in a cross. In a cross of Stoneville 20 × highly resistant Deltapine, the resistance was dominant, while the resistance in a cross of Stoneville 20 × susceptible Acala was inherited as a recessive trait. In a cross of Stoneville 20 × Stoneville 2B with a low level of resistance, no dominance was observed. In the F2 population, some plants were resistant to race 1 but susceptible to race 2 or vice versa, while other plants were resistant to both races. Based on a half diallel crossing involving six Upland parents in Africa, Innes et al. (1974) indicated that the behavior of the B7 gene was not consistent with that of a simple Mendelian locus with incomplete dominance.

However, in an interspecific cross and backcrosses between Stoneville 20 (grade 6–7) and G. barbadense Sakel (grade 12) in Sudan, Knight (1953b) observed that resistance in the progeny was dominant with a 1R (grade 8–10):1S (grade 12) ratio in BC1F1 and a 3R:1S ratio in F2 of BC2, BC3 and BC4. Therefore he assigned B7 for the resistance gene in Stoneville 20. He further showed that B7 was non-allelic to B1-B6 because susceptible plants were observed in F2 populations from crosses between Stoneville 20 and G. barbadense BAR2/11 (B1B1), BLR14/16 (B2B2), BAR14/9 (B3B3), BAR14/19 (B4B4) and BAR14/20 (B5B5). The testcross between F1(Stoneville 20 × B2-carrying BLR14/16) and Sakel showed 2 (4–7 grade):1 (8–9 grade):1 (12 grade) ratio and 15 (3–7 grade):1 (8–10 grade) ratio in F2 of Stoneville 20 × B2-carrying BAR 7/1. Based on the observation that the level of resistance in Stoneville 20 was reduced during the backcross process, Knight (1953b) suggested that the resistance in Stoneville 20 was due to the presence of the major gene B7 accompanied by minor resistance genes.

b 8

Resistant wild diploid B genome G. anomalum (grade 2–4) was crossed with susceptible the A genome G. arboreum cultivar Java (grade 8–9), and then backcrossed to Java to transfer BB resistance to the cultivated diploid species (Knight 1954). Resistance was recessive, but the typical 1R:3S segregation ratio for BB responses was not observed in BC1F2, BC1F3, BC1F4, BC2F2 and BC3F2. Nevertheless, Knight (1954) assigned b8 to the gene transferred from G. anomalum to G. arboreum, and further, he showed that b8 was closely linked to R2 (a petal spot gene on chromosome A07) at a recombination frequency of 1.4%. Because the behavior of b8 was distinctively different from that of the other seven B genes, Knight suggested that b8 was not allelic to any of them. It is unknown if this resistance was ever transferred into cultivated tetraploid cotton.

B9K and B9L

Through repeated backcrossing up to BC7, Knight (1963) successfully transferred two partially dominant resistance genes from the Indian G. herbaceum cultivar Wagad 8 (after chromosome doubling) to Sakel (G. barbadense). The gene with a stronger resistance effect, designated B9, conferred resistance ranging from grade 5–6 when homozygous, to grade 7–8 when heterozygous, and segregated in the typical 3R:1S ratio in the F2. B9 was non-allelic to other B genes, because when homozygous backcross plants possessing B9 were crossed with Sakel lines possessing B2, B3, B4, B5, or B7, a typical 15R:1S ratio was observed in the F2. The gene with a weaker level of resistance, when homozygous, gave a range of 7 to 8 grade (when heterozygous, it gave 9–12 grade). However, no gene symbol was assigned to this gene with the low level of resistance, because gene homology tests were not performed. Innes (1965a) later confirmed the presence of B9 and minor genes in Wagad 8 following a cross to susceptible G. herbaceum var. africanum ‘ET’s.

Perhaps without knowing Knight’s work on B9 and B10, Lagiere (1960), while working in French-speaking Africa, named B9 and B10 to the two major BB resistance genes identified in resistant Upland Allen 51-296. Innes (1965a, b) confirmed that the high resistance in Reba W 296 (derived from Allen 51-296 and purported to be homozygous for B9B10) was due to the major gene B9, and a number of minor genes with additive effects. However, the Lagière's B9 was not homologous to Knight's B9 and was also independent of other B genes, because susceptible plants (in a 15R:1S ratio, except B6) were observed in F2 populations of crosses between Bar 11/13 (a resistant line from the F3 of Reba W296 × susceptible Sudan Upland XA 129) and Upland Bar lines each possessing B1, B3, B5, B6, or B7. F2 populations of crosses between Bar 11/13 and Sakel type Bar 14 lines (G. barbadense) each possessing a different B gene (B1 to B7, B9 and Bherb) also produced a 15R:1S ratio. Thus, the symbols B9L and B9K were assigned to the two different resistance genes from the Lagiere and Knight sources, respectively (Innes 1965b). Innes (1966) observed that, while the leaf resistance of B9K Sakel was high, its stem resistance was of a low level and suggested that leaf, stem and boll resistance may be under the same genetic control in some crosses but not in others.

B10K and B10L

In a plant protection conference held in London in 1956, Knight reported B10, a partially dominant resistance gene identified in G. hirsutum var. punctatum Kufra Oasis in Libya (Knight 1957). However, no details could be found in the literature. Due to different sources of Knight’s and Lagiere’s B10, Innes (1965b) proposed symbols B10L and B10K for the two B10 genes of the same sources as B9K and B9L, respectively, although allelic tests were not made.

B 11

Innes (1966) assigned the previously unnamed gene with a weaker resistance (designated Bherb by Innes 1965c) transferred by Knight (1963) from G. herbaceum Wagad 8 to Sakel as B11, because it was non-allelic to other B genes based on gene homology tests between B11 and other B genes. He also confirmed the presence of strong environmental effect on the expression of B11 and noted that B11 was much more effective in the Upland background than in Sakel (G. barbadense), but the opposite was true of B9K.

B 12

Crosses with Upland S295 in Paraguay and France resulted in segregations for BB resistance to race 18 and 20 (Follin et al. 1988). They concluded that resistance to each race was dominant and controlled by one gene and that Upland S295 (resistant to both races) possessed a major gene for race 18 and a minor gene for race 20, but the two genes were tightly linked. Wallace and El-Zik (1989) confirmed that the resistance in S295 to a mixture of US races (1, 2, 7, and 18) and African HV1 (race 20) was dominant and controlled by the same resistance gene, designated B12, or two closely linked genes, from crosses with Tamcot CAMD-E (resistant to race 1, 2, 7 and 18 but susceptible to race 20) and Stoneville 825 (susceptible to all the above races). A 3R (1–3 grades):1S (4–10 grades) ratio in F2 progenies and 1R:1S ratio in BC1F1 progenies were observed. The responses in cotyledons and true leaves were correlated, indicating that resistance in cotyledons and true leaves was controlled by the same genetic mechanism. This was further confirmed by Wright et al. (1998) based on an F2 population derived from S295 × highly susceptible Pima S-7 (G. barbadense) and Xiao et al. (2010) using an intraspecific Upland population of resistant Delta Opal × susceptible DP388 infected with race 18.

BIn, Bn, and Bs

Green and Brinkerhoff (1956) in Oklahoma reported that the resistance in Upland breeding lines 1-10-B-4-B, 20-8-1-3-1, and 6-77-5-8 was controlled by single dominant genes, BI, BN, and Bs, respectively. Line 1-10-B-4-B was derived from a resistant plant of an unknown cultivar found in a farmer’s field near Indiahoma, OK, and the F2 resulting from a cross with Stoneville 20 gave a 13R:3S ratio, indicating segregation for 1 dominant (designated BI from line 1-10-B-4-B) and 1 recessive gene (b7 from Stoneville 20) for resistance. Line 20-8-1-3-1 was selected from Northern Star, and the F2 resulting from a cross with 1-10-B-4-B (BI) segregated in a 15R:1S ratio, indicating a different dominant gene (designated BN) in 20-8-1-3-1. Line 6-77-5-8 was selected from Upland Stormproof No. 1, and its F2 with 1-10-B-4-B (BI) gave a 15R:1S ratio, indicating another different dominant gene, designated BS. However, the F2 of 6-77-5-8 (BS) × 20-8-1-3-1 (BN) did not give a 15:1 ratio but produced more resistant plants (595R:14S) than expected, and all F3 plants were resistant. Results indicated that BI was independent of b7, BN and Bs, but BN and BS could be the same or closely linked gene. The authors stated that studies were in progress to clarify the relationship of the above genes; however, no follow-up reports were published. Therefore, their allelic relationships with one another and with other B genes are currently unknown. To avoid confusion with B1, BI was later renamed as BIn.

BSm and BDm

Bird and Blank (1951) showed that the Upland Deltapine cultivar had a higher degree of tolerance than two other Upland cultivars- Stoneville 2B and Acala. The F2 progenies from a cross of Stoneville 20 with Deltapine displayed a higher degree of BB resistance than the F2 offspring from a cross of Stoneville 20 with Acala, although both crosses inherited the same major gene (B7) for resistance from Stoneville 20. This led them to suggest that the susceptible parents may possess different numbers of minor genes for resistance which influenced the degree of resistance produced by the major gene. In a follow-up study, Bird and Hadley (1959) showed that Stoneville 20 contained two effective genetic components determining its BB resistance: one is the major gene B7 and the other a constellation of minor genes designated BSm, which was also found in Stoneville 2B. Deltapine, however, possessed another composite component BDm, while Acala had no effective resistant component. Therefore, the cultivars used in the study were assigned the following genotypes: Stoneville 20, B7B7BSmBSmbDmbDm; Deltapine, b7b7bSmbSmBDmBDm; Stoneville 2B, b7b7BSmBSmbDmbDm, and Acala, b7b7bSmbSmbDmbDm. However, the composite components in Stoneville 20 and Stoneville 2B may not be identical. The genes were additive and the effect of the major gene (B7b7) was greater and less influenced by environment in the presence of the two B-m genes of the composite components than in the presence of one. There was no evidence of linkage between genetic factors controlling Stoneville 20 resistance.

Other unnamed BB resistance genes

In addition to B9 and B11 in Wagad 8 (G. herbaceum), Innes (1965a) detected another major resistance gene in a Chinese indigenous diploid variety (G. herbaceum), and the gene was not homologous with B9 from the same species. However, no symbol was given to this gene.

In his Ph.D. study, Owen (1967) in the US performed a genetic study of BB resistance in five resistant lines of American Upland cotton based on F1, F2, backcross and F3 generations in the field and in growth chambers. Resistance was incompletely dominant in all five lines, and segregation results indicated one resistance gene in three lines, two genes in another line and several genes in the other line. There was also evidence for additional genes providing a greater degree of resistance. However, no follow-up studies were published. Brinkerhoff et al. (1979) in Oklahoma reported that the BB resistance in a moderately resistant mutation, induced by irradiating seed of a susceptible Westburn 70 with fission neutrons, was due to a single dominant gene, different from B3, B4, B5, b7, or BN.

Based on the observations of seven resistant, moderately resistant and susceptible Upland parents and their F1 and F2 populations evaluated in the field, Singh et al. (1987) in India reported that resistance to BB was incompletely dominant and that the cultivars studied differed for two resistance loci. Sajjad et al. (2007) in Pakistan showed that the BB resistance to race 18 in two breeding lines—C2 (67) 577 and C2 (69) 1455, in crosses with susceptible DPL-7340-424, was dominant and controlled by a single resistance gene at both seedling and adult stages. The resistance gene in the two resistant lines was the same, as no susceptible segregants were observed in their F2 and backcross progenies. However, it is unknown if the gene was the same as B12. Based on a testcross and F2 population, Sajjad et al. (2003) showed that the gene for resistance to BB and the gene for resistance to cotton leaf curl virus were linked with a recombination frequency of 25.9–32.8%.

B gene combinations

Due to the fact that a single B gene was either ineffective in conferring BB resistance to a predominant Xcm race, or that new Xcm races developed rapidly to defeat single B genes, pyramiding of two or more B genes in one cultivar or line has been vital to breeding for BB resistance (Table 2). Knight developed different B gene combinations in his breeding and genetic work for BB resistance in Sudan. He showed that, in the G. barbadense Sakel background, B2 gave a resistance of grade 5–7, and B3 gave a 4–7 grade, but the B2B3 combination gave grade 3. Interestingly, the genes B2B3 were more effective in conferring BB resistance when transferred to an Upland genetic background than in the Sakel (G. barbadense) background. His work was continued by Innes in the 1960s. Innes (1964) compared BB resistance in F2 families from diallel crosses involving Sakel homozygous for each of the B genes, B1 to B7, and showed that the best resistance was conferred by B2B6, closely followed by B1B4, B2B4, B3B6, and B4B6. Also exhibiting additivity, but conferring intermediate resistance was B1B3, B2B3, B3B4, B3B5, B4B5, B4B7, B5B6, and B5B7. B1 and B4 were transferred to the Upland Wilds Sus 16/1, which was found not to be absent of the db gene for dwarfing. B7 was more effective when transferred to Acala 4-42 than in Wilds Sus 16/1. B1 and B5 were each able to increase the resistance of the Upland Wilds Sus 16/1 when transferred, but B1 was more effective, demonstrating the importance of genetic background. In a set of diallel crosses between seven Bar lines of Sakel, each homozygous for one B gene in the series conferring BB resistance, Innes (1965d) showed that the combination B2B9 produced resistance as high as that given by B2B6. B4B6 and B1B9 also conferred high resistance. A cross between a line carrying B6 and one having a weak resistance gene derived from G. herbaceum, designated Bherb (B11 later on) also showed high resistance. The B6 × Bherb cross gave a high resistance rating but its F2 generation showed two types of families with differing resistance, indicating that a third gene was probably present.

Table 2 B gene combinations and associated germplasm for bacterial blight resistance in cotton
Full size table

While breeding for BB resistance at Shambat, Sudan, Innes (1961) demonstrated that needle inoculation of the main vein of the leaf under greenhouse conditions was a useful supplementary procedure in transferring the modifier B6m, both alone and in combination with B2 (B2B6m). The mean lesion length from this inoculation technique was used to distinguish between homozygotes for B2 and B2B3; however it could not differentiate between B2 and B2B3 types in segregating progenies. Environmental changes also influenced the difference in mean lesion length between B2 and B2B3 resistance, such that differences were detected at Shambat, but not at Wad Medani. In the field, B2B3 resistance is more effective than B2 alone. Innes (1963b) observed the greatest loss of field BB resistance occurred in Bar 14/25 (B2B3Sakel). The breeding lines B2Sakel, Bar 14/16, and B2B3 Upland, and Bar 11/7 also showed decreased field resistance, but not the corresponding B2 type Bar 1 and Knight's B2B3punctatum; and Bar 3/5 also maintained its resistance. Bar 3/5 and Bar 11/7 differed only in modifier genes. Innes (1974) summarized his work in Sudan on inoculation experiments for a wide range of Egyptian cotton (G. barbadense) lines homozygous for single genes and for digenic and trigenic combinations of Knight's B genes for BB resistance. Although leaf inoculation was successful, stem inoculation was only partially so, and boll inoculation, using two different techniques, failed to produce measurable disease symptoms. There was a good general relationship between leaf and stem resistance, and a close association between resistance to natural attack in the field and leaf resistance to artificial inoculation. The strong resistance conferred by B2B9K, which was as effective as B2B6 or B2B3B6, was confirmed. No other combination was as effective when inoculated artificially. Nevertheless, in a natural field infestation, only mild symptoms were found in lines homozygous for B1B9K and for B4B6. Under the same conditions, lines with B2B6 showed no symptoms, but those with B2B3 were severely attacked.

During the 1950s in Texas, Bird transferred B genes to different Upland cottons including Empire and Deltapine from Knight’s B gene containing Sakel (G. barbadense) strains by backcrossing and inbreeding. In 1960, he developed an immune Upland line 101-102B (carrying B2B3BSm) through interspecific introgression (Bird 1960). He used Upland Empire WR (containing BSm) as the recurrent parent to cross and backcross for five generations with B2B3-containing Bar 4/16 (G. barbadense), followed by crossing to a possible b7-containing Upland MVW. In each backcross, the most resistant plants were selected for further backcrossing after screening with a mixture of Xcm races. Immune plants were only observed after several backcrosses. Through this process, Bird developed many Tamcot lines with high levels of BB resistance possessing different B gene combinations, including B2B3B4 and B2B3B4b7 conferring immunity against all known BB races in the US (e.g. Bird 1976, 1979a, b). In Oklahoma, an immune line, Im 216, was developed by Brinkerhoff (Brinkerhoff et al. 1984), as a selection from a segregating population of Bird’s B2B3 Empire (one of the parental populations used to develop 101-102B), after several generations of inbreeding and selection for resistance to a mixture of races 1, 2, 4, and 10. The immunity of Im 216 was completely dominant and thought to be due to B2B3B7, because the F2 data from a cross between Im 216 and fully susceptible Acala 44 fitted a segregating ratio for two dominant and one recessive independently inherited genes. Several fully susceptible F2 plants also showed segregation of resistance, indicating the existence of the recessive resistance gene b7. However, the F2 progeny also fitted a segregating ratio for two independent dominant genes.

El-Zik and Bird (1967) reported that the B4 gene was the most effective factor, followed by B2B3, B2B3B7, B2B6m, and B7 when Upland cotton was inoculated with race 1, race 2, or their mixture. El-Zik and Bird (1970) confirmed that B4 gave a higher level of BB resistance than did B2, B3, or B7 against five BB races and was as effective as B2B3B6. In the Empire background, B4 was more effective than B2B6, B2B3, or B2B3B7. However, B4 may be not as effective in other genetic backgrounds or testing conditions. Essenberg et al. (2002) in Oklahoma reported the development and genetic characterization of four near-isogenic lines (NILs) of Upland, each carrying one of the single homozygous BB resistance genes, B2, B4, BIn, or b7. The NILs were derived from at least six backcrosses to the susceptible recurrent parent Acala 44, followed by single plant-progeny row selection for uniformity. In the Acala 44 background, B2, B4, and BIn are partially dominant genes, and b7 is partially recessive. Resistance to race 1 was ranked as B4 ~ b7 > BIn ~ B2. Essenberg et al. (2014) used these NILs to develop gene-pyramid lines with all possible combinations of two and three B genes. Isogenic Xcm strains carrying single avirulence (avr) genes were used to identify plants carrying specific resistance B genes. Under field conditions in north-central Oklahoma, pyramid lines exhibited broader resistance to individual races and, consequently, higher resistance to a race mixture. It was predicted that lines carrying two or three B genes would also exhibit higher resistance to race 1, which possesses many avr genes. However, they did not approach the level of resistance of Im 216. In a growth chamber evaluation, Im 216 (carrying B2B3B7) exhibited considerably lower bacterial populations than any of the one- (such as B4), two-, or three-B-gene (such as combinations with B4) lines.

Genes conferring BB resistance may be associated with resistance to other diseases in cotton. Brinkerhoff and Hunter (1961) in Oklahoma first noted that BB resistant lines contained a much higher proportion of Fusarium wilt resistant plants than susceptible populations. However, the association of resistances to different diseases may be breeding population specific. Cauquil and Follin (1970) in Africa studied boll rot resistance in three American Empire WR genotypes and seven Central African Upland lines differing in BB resistance. Results suggested that lines possessing major genes for BB resistance (B2B3 and B2B3B6m) exhibited greater resistance to fungal boll rot than lines lacking these genes. Resistance mechanisms associated with the pericarp were more effective in the B2B3B6m genotype than in the B2B3 genotype, indicating that the presence of the modifier gene B6m in association with B2B3 further improved resistance to boll rots. However, the B6m gene had less effect on resistance mechanisms located within the boll. Results showed that boll rot resistance located in the pericarp was greater when two major genes (B2B3 or B9B10) were present, while a single resistance B gene was ineffective. Bird (1972) confirmed that resistance to five diseases, including BB resistance, was interrelated with common resistance genes. Bird (1982) further reported that BB resistance had the strongest association with resistance to Fusarium wilt/root-knot nematode complex and a lower association with resistance to Verticillium wilt, Phymatotricum root rot and seedcoat resistance to mold. These studies led to the development of the multi-adversity resistance (MAR) program at Texas A&M University (Bird 1982, 1986), and the release of numerous MAR germplasm and cultivars (e.g. Bird 1979a, b; El-Zik and Thaxton 1996, 1997; Thaxton and El-Zik 2004). However, the relationship between resistance to BB and Fusarium wilt in MAR lines could not always be verified by independent studies. For example, Tamcot Sphinx, a MAR line with resistance to BB, was listed as moderately resistant to Fusarium wilt on its plant variety protection certificate (#009600134). In a Fusarium wilt infested field in Gaines county, TX, with moderate Fusarium wilt and high root-knot nematode pressure, this cultivar had Fusarium wilt symptoms that were more severe than any other cultivar tested (Wheeler and Gannaway 1998). Major resistance genes for BB and quantitative resistance genes for other pathogens, were presumably pyramided in some of the MAR germplasm lines. However, the concept currently lacks evidence to suggest that resistance genes for different pathogens, including Xcm and Fusarium wilt, are the same, or even linked on the same chromosomes.

Quantitative genetics

Since the reactions of cotton plants to Xcm infections can be quantified in the field or greenhouse based on a rating scale such as 0 to 12 in Sudan, and 1 to 10 in the US, quantitative genetic techniques, such as F2 and parents, generation-mean analysis, and diallel analysis, have been used to investigate the genetic basis of BB resistance (see Table 3 for a summary). Bird and Hadley (1959) used a generation-mean analysis to evaluate parents and their F1, F2, F3, BC1P1 (i.e., F1 × P1) and BC1P2 (i.e., F1 × P2) between the resistant parent Stoneville 20 (known to carry B7), and three susceptible parents for resistance to race 1 and 2. Only additive variance in each cross was detected with a moderate heritability (0.45–0.50), and the resistance in Stoneville 20 was conferred by two effective genetic components determining resistance, i.e., major gene B7 and minor gene BSm. Wallace and El-Zik (1990) employed the generation-mean analysis to investigate resistance to three new isolates (highly virulent race 20 of Xcm from central Africa) in three resistant Upland lines (Tamcot CAMD-E, LEBOCAS3-80 and S295), susceptible Stoneville 825, and their F1, F2 and backcross progenies based on their responses in cotyledons and/or true leaves. The results showed that resistance was dominant with a duplicate type of digenic interaction, but additive effects were predominant as the narrow-sense heritability estimates ranged from 0.59 to 0.68. In four F2 crosses, Wright et al. (1998) estimated a higher broad-sense heritability for BB resistance including: 0.91 for resistance to races 2 and 4 in Empire B2 × Pima S-7; 0.79 for resistance races 2 and 4 and 0.58 for resistance to race 18 in Empire B2 × Pima S-7; 0.91 for resistance to races 2 and 4 and 0.95 for resistance to races 7 and 18 in Empire B2b6 × Pima S-7; and 0.97 for resistance to races 2, 4, 7 and 18 in S295 × Pima S-7. It is worthwhile pointing out that the above three studies, in a span of 40 years, were all conducted by the same research program at Texas A&M University.

Table 3 Quantitative genetics of bacterial blight resistance in cotton
Full size table

Most quantitative genetic studies in BB resistance have been based on diallel crossing schemes. In the same Texas A&M research program, El-Zik and Bird (1967) conducted an 8-Upland parent (each carrying a different B gene or combination) diallel study for resistance to BB races 1, 2 and a mixture of both races over 2 years. The diallel was comprised of four breeding lines—146-25 (B4), 34G (B2B3), 91-92A (B2B3B7) and 14G (B2B6m), highly resistant to both races 1 and 2, and four other parents- Austin 7 (B7, resistant to race 1), Empire WR (BSm), Deltapine TPSA (BDm), and Texacala (with no known major B genes, susceptible to both races). The Hayman–Jinks diallel genetic analysis showed that both additive and dominant variance components were significant with a mean dominance of 0.84–0.93, suggesting that BB resistance was partially dominant but approaching complete dominance. The minimum number of genes for BB resistance was estimated to be one. Innes and Brown (1969) used Uplands Reba W296 (with B9L), Bar 7/1 (B2), Bar 24/5 (B7), Bar 11/11 (B6) and Acala 4-42 (b) to make a 5 × 5 diallel, and used the Hayman–Jinks genetic model to analyze data of the parents and both F1 and F2 evaluated in Sudan for leaf resistance, and parents and F2 for leaf and boll resistance in Uganda. Results showed that only the additive variance component was significant, and the authors concluded that additivity, together with partial dominance, accounted for most of the genetic variation in BB resistance. While epistasis was not detected, there was a strong interaction in the B2 × B6 cross. Among the five parents, Reba W296 had the highest number of dominant alleles for BB resistance. In a follow-up experiment on both F1 and F2, in a half diallel from six Upland parents, including three different parents inoculated with two isolates in Sudan (two locations) and Uganda, Innes et al. (1974) studied the genetic variation of BB resistance based on Hayman–Jinks and Allard models. These parents possessed different B genes or combinations, including three Sudanese Uplands—Bar 7/1 2 (B2), Bar 24/5 3 (B7) and Bar 12/16 (B2B6) and three US Uplands—101-102B (B2B3BSm), Acala 1517BR (B7) and Acala 4-42 (no resistance B gene). Additive effects were most important, and non-additive effects were due to the dominance effect. Evidence suggested that minor genes affected the behavior of B7 and enhanced the resistance conferred by B2B3. The behavior of the B7 gene was not consistent with its being a simple Mendelian locus with incomplete dominance. Genetic variances varied depending on inoculum, being lower with one Xcm culture than with another. Since 101-102B possessed a polygenic complex, in addition to genes B2 and B3, progeny of 101-102B showed that resistance built up through selection of minor genes could be effectively transferred. In studying 10 Upland parents and their 45 F2 progenies for BB resistance, Singh et al. (1989) in India showed that parent 101-102B had the greatest number of dominant alleles for resistance to BB. The Hayman–Jinks genetic model was used by Luckett (1989) in Australia in a half diallel of 10 Upland parents, which included three resistant lines- Siokra (derived from Tamcot SP37, carrying B2B3B7) and Reba P279 (carrying B2B3B9L). Both additive and dominance effects were detected for BB resistance, but resistance was determined primarily by additive effects with heritability estimates of 0.81 for F1 and 0.76 for F2.

The above generation-mean and diallel analyses estimated moderate to high heritabilities for BB resistance. However, using Griffing’s approach to analyse a complete diallel with 56 F1 hybrids from eight Upland parents from Cameroon, Côte d'Ivoire, Togo and Chad, Bachelier et al. (1992) in Chad detected the existence of specific combining ability (SCA) with a low heritability (0.24) for BB resistance. F1 susceptibility was significantly higher than that of the parents, suggesting the existence of residual heterozygosity in certain parents. In a glasshouse study in New Mexico, Mahill and Davis (1978) evaluated BB resistance in seedlings of 28 F1 hybrids from a North Carolina Design II, between 7 male and 4 Upland female parents. The 7 males included six G. barbadense lines—susceptible Pima S-4, Pima 8, E1124, and E1097 and resistant B2B6 × Pima 32 and K0210 and one resistant Upland Albar 637. The 4 Upland female parents included resistant strain 1–8 and susceptible Acala 4-42, and their cytoplasmic male sterile counterparts. Variances due to female and male parents (from additive effects) and female × male interaction (from SCA) were significant, and SCA was due to partial dominance effects. Resistant male parents B2B6 × Pima 32, Albar 637, and K0210 showed no difference in combining abilities, indicating equal effectiveness as sources of BB resistance.

Cytoplasmic effects

Because the tetraploid Upland cotton share a cytoplasm, similar to its cytoplasm donor—cultivated diploid species—G. herbaceum and G. arboreum (Wendel 1989), it was not surprising that Bachelier et al. (1992) did not detect any reciprocal effects in their complete diallel crosses using eight Upland parents. However, exotic cytoplasms from other Gossypium species may affect cotton growth and responses to abiotic and biotic stresses. Mahill and Davis (1978) demonstrated that G. harknessii cytoplasm enhanced BB resistance by 12%, as compared to Upland cytoplasm. Mahill et al. (1979) further showed that cytoplasms from G. berbaceum and G. barbadense slightly increased BB resistance, as compared to the cytoplasm from Upland cotton.

Molecular mapping of BB resistance genes

Wright et al. (1998) first used restriction fragment length polymorphism (RFLP) markers to map B2, B3, b6 and B12 genes. Four F2 populations, from crosses between susceptible G. barbadense Pima S-7 and four resistant Upland lines—Empire B2, Empire B3, and Empire B2b6 and S295, were used in the quantitative trait locus (QTL) mapping analysis. Seven QTL were identified including, one (corresponding to B2) flanked by RFLP markers pAR 335b and G1219 (explaining 98.0% phenotypic variation for resistance to races 2 and 4) within a 4.3 cM region on chromosome c20 (LGD08) in the Empire B2 × Pima S-7 F2 population. In the Empire B3 × Pima S-7 F2 population, a RFLP marker pGH510a, located near the end of chromosome c20, explained 88.2% of the phenotypic variation in resistance to races 2 and 4. An earlier cytogenetic analysis also mapped B3 to the end of the same chromosome (c20). Interestingly, the B3 locus explained 53.4% of the phenotypic variation in resistance to Xcm races 7 and 18. In the Empire B2b6 × Pima S-7 F2 population, similar to the Empire B2 × Pima S-7 F2 population, the region (B2) between the G1219 and pAR335 explained 92.2% of the phenotypic variation in resistance to races 2 and 4. Interestingly, in this cross, four additional QTLs, which explained 56.4% of the phenotypic variation in reaction to races 7 and 18, were identified. These QTL corresponded to the recessive b6 allele, b6a on LGD02 (formerly LGU01), b6b on c5, b6c on c20 (formerly LGD04), and b6d on c14. The authors suggested that the region near marker pAR1-28 on chromosome c5 mapped to a region that is homoeologous to the B2 locus on chromosome c20. The authors further suggested that this region may correspond to the BB resistance gene B4, identified in the diploid A genome species G. arboreum, and assigned to chromosome c5 using cytological stocks (Endrizzi et al. 1985). In the S295 × Pima S-7 F2 population, B12 was mapped to a region near the DNA marker pAR043 within 11.4 cM on chromosome 14. This QTL accounted for 94.2% of the phenotypic variation in resistance to BB races 2, 4, 7, and 18. Although no closely linked RFLP markers were identified, results from this study have paved the way for follow-up genetic mapping studies focused on B12.

Australia was very successful in incorporating BB resistance into commercial cotton cultivars (Kirkby et al. 2013). Pedigree records suggest that the resistance source was a set of related, so-called immune lines carrying the B2B3B7 and BSm genes. The Australian resistant Upland cultivar, CS50, in an interspecific cross with susceptible Pima S-7, showed that resistance to race 18 segregated as a single dominant locus (Rungis et al. 2002). Using mapped RFLP markers in the interspecific cross, Rungis et al. (2002) suggested that the resistance locus for race 18 is not located on chromosome c20 near the B2 or B3 genes, as previously mapped by Wright et al. (1998), but co-segregated with a RFLP marker on chromosome c14. This marker is known to be linked to B12, a gene originally from African cotton cultivars that provides broad-spectrum resistance to BB.

Xiao et al. (2010) at Monsanto reported closely linked portable PCR-based markers for B12. In an F4:5 population of 285 families from an intraspecific Upland cross between race 18 resistant Delta Opal and susceptible DP 388, four closely linked simple sequence repeat (SSR) markers (CIR246, BNL1403, BNL3545, and BNL 3644) flanking B12 in a 5.6 cM region were identified. These SSR markers, in turn, were further used to identify four single nucleotide polymorphism (SNP) markers (NG0207069, NG0207155, NG0210142, and NG0207159) spanning 3.4 cM that flanked the B12 region on c14. The primer sequences for the above SSR and SNP markers are listed in Table 4. Through a bulk segregant and segregation analysis in an F2 population of 127 plants from Delta Opal × BRAS ITA 90 in Brazil, an 80 bp SSR marker, amplified by the BNL 2643 primers, was identified to be associated with the resistance in Delta Opal (Marangoni et al. 2013). However, Silva et al. (2014) reported that the 146 bp SSR marker from the CIR246 primers was not only PCR amplified in B12-carrying S295 and Delta Opal, but also amplified in cotton carrying B2B3 (101-102B) and B9LB10L (Guazuncho-2). Thus, both segregation and molecular analysis indicated that B12 in S295 was closely linked to the B2B3 locus which was homologous to or co-segregates with the B9LB10L locus. Therefore, the CIR246 marker could be useful in identifying alleles for resistance up to races 1–18 but cannot be used to discriminate gene or gene complex involved in resistance within the same chromosomal region.

Table 4 Primer sequences for SSR and SNP markers linked to B12 with resistance to bacterial blight race 18
Full size table

Using an interspecific F2 population of S295 × Pima S-7 and the genome sequence of G. raimondii, Yang et al. (2015) delineated the B12 gene to a 354 kb region containing 73 putative plant disease resistance genes. Most recently, Zhang et al. (2019) has further narrowed the B12 gene to a region containing only a few putative genes using 550 multiparent advanced generation intercross (MAGIC) lines and more than 500,000 genotyping-by-sequencing based SNP markers (Thyssen et al. 2019; Zhang et al. 2020).

Elassbli et al. (2019) performed a genome-wide association study for more than 330 US Upland germplasm accessions based on a total of 26,345 SNPs from the CottonSNP63K array. A total of 55 SNPs on 9 chromosomes (c1, c5, c8, c10, c14, c15, c20, c22, and c24) were found to be associated with resistance to BB race 18, and each explained 13 to 52% of the phenotypic variation. Chromosomes c5, c14 and c24 had the highest number of SNPs associated with BB resistance. The QTL regions on c5, c14, and c20 are likely those reported by Wright et al. (1998).

Marker-assisted selection

Amudha et al. (2003) in India reported the use of random amplified polymorphic DNA (RAPD) markers to track the introgression of BB resistance gene from G. anomalum into Upland MCU5 and identified two RAPD markers. However, the SSR marker CIR 246 identified by Xiao et al. (2010) was proven to be most useful. Three SSR alleles (146,156, and 166 bp) were amplified by the CIR 246 primers. Xiao et al. (2010) showed that, two lines (03Q060 and X 3163) with the homozygous 146 bp alleles were all resistant; 5 heterozygous allele cotton genotypes including PMX 1144 and 660 with 146 bp and 156 bp or 146 bp and 166 bp were segregating in resistance; and 6 homozygous 156 bp lines including Acala Maxxa or 166 bp genotypes or 3 heterozygous 156 bp/166 bp genotypes including X9269 were all susceptible. The presence of the ‘resistance’ 146 bp allele was consistent with the SNP haplotype (A–C–T–T) from four SNP markers in all the nine resistant lines, while the susceptible allele 155 bp or 165 bp was consistent with the SNP haplotype (G–G–C–A) in all the nine susceptible lines tested. Silva et al. (2014) further showed that the CIR246 SSR primers amplified the 146 bp fragment in race 18 resistant S295 (carrying B12), Delta Opal (carrying B12), 101-102B (carrying B2B3BSm) and Guazuncho-2 (carrying B9LB10L), while the 156 bp fragment was amplified in race 18 susceptible Memane B1 (carrying B2BSm) and ST 2B-S9 (carrying BSm), and the 166 bp fragment was amplified in susceptible Acala 44 carrying no known B genes. Due to outcrossing over generations, advanced breeding lines as well as commercial cultivars, may no longer be homozygous for resistance to race 18. Faustine et al. (2015) used the SSR marker CIR 246 (1.8 cM from B12) and SNP marker NG0207155 (0.6 cM from B12) to screen individual plants in three Tanzania and four Brazilian Upland cultivars and found that the resistance gene B12—linked marker allele frequency ranged from 69–75% for UK91 and 25–86% for UK08, and to 0% for Cedro. Results suggested that the cultivars tested were not homozygous in the B12 locus. Wheeler et al. (2016) reported that water soaked symptoms of susceptibility were found in 8–15% of the seedlings in resistant transgenic cultivars PHY 375WRF, FM 1830GLT and FM 2484B2F when inoculated in the greenhouse.

Summary and concluding remarks

There are currently 20 races of Xcm recognized in bacterial blight of cotton, and these have been effectively controlled in many cotton-producing countries by planting resistant cultivars. However, the disease has resurged in recent years in the US due to the popularity of susceptible, transgenic cultivars. Since the 1940s, more than 20 major resistance B genes (B1 to B8, B9K, B9L, B10K, B10L, B11, B12, BIn, Bn, Bs, and more than 4 unnamed genes), and at least two polygene complexes (BSm and BDm), have been identified. Actions of the resistance B genes may be dominant, partially dominant, or even recessive, with additive or epistatic effects, depending on B genes. Many major B genes can be detected using quantitative genetic approaches. One B gene may be resistant to one or multiple Xcm races, and pyramiding of several B genes can enhance resistance to one or multiple Xcm races. However, allelic relationships and interactions among some of the B genes are currently unknown. For example, the exact chromosomal locations of most of the B genes including B2B3 have not been determined. Although the notion that there are two complexes (BDM and BSM) has been widely accepted by the cotton community, no further work has been attempted to clarify their existence, and their relationship with one another, and with other B genes. In addition, other major resistance B genes have been identified in germplasm lines in the US, India and Pakistan, but no allelic tests were performed.

Many B genes in tetraploid cotton were identified in resistant lines selected from susceptible cultivars. Residual genetic variation in obsolete lines and as well as modern transgenic commercial cultivars exist, due to heterozygosity or natural outcrossing. Some lines may not be homozygous in their resistance or susceptibility to BB. Therefore, pedigree selection within existing susceptible cultivars is not out of date and should still be an effective way to identify BB resistant genotypes.

Genetic resources possessing different B genes should be collected and well maintained. Resistance to BB exists in both wild and cultivated diploid Gossypium species and should be transferred to cultivated tetraploid cotton. For examples, many accessions of G. arboreum and G. herbaceum are known to be immune to BB; however, no introgressed Upland or G. barbadense lines with immunity have ever been developed and reported. Because susceptible G. arboreum and G. herbaceum lines exist, genetic and molecular studies can be performed to identify B gene(s) that confer immunity in crosses within the diploid species. Markers can then be used to trace their transfer to Upland cotton through interspecific hybridizations.

Although it is difficult to perform allelic tests among all the B genes, gene mapping using molecular markers should provide a quick avenue to locate them onto chromosomes. Among the B genes, B12 appears to confer resistance to most of the Xcm races, including races 18 and 20, and therefore, B12 is the focus in current breeding and genomic studies for BB resistance. Markers closely linked to B12 have been developed and can be used for marker-assisted selection in BB resistance. Candidate genes for B12 have been further identified through high resolution molecular mapping using SNP markers. Currently, however, no B genes have been cloned, isolated and sequenced. It is expected that B12 will soon be cloned and sequenced, facilitating a better understanding of the molecular genetic basis of bacterial blight resistance in cotton.