Introduction

Rice is cultivated all over the world with a wide range of variation in geography. Compared with the tropical and subtropical regions, rice grown in temperate and high altitude regions is frequently exposed to low temperature during the growing season. Cold stress is a major constraint to rice cultivation in 25 countries, including the United States (Yoshida 1981; Pereira da Cruz et al. 2013). Although rice is sensitive to cold stress, wide range of genetic variation for cold tolerance exists in rice germplasm (Baruah et al. 2009; Bosetti et al. 2012) and indica cultivars are less tolerant than the japonica cultivars (Andaya and Mackill 2003).

In direct seeded rice, germination ability, early seedling emergence, and seedling vigor are crucial for rapid and uniform crop establishment, and increased ability to compete with weeds in rainfed and upland rice cropping system. Staggered germination results in variation in maturity resulting in rice crop with poor quality. Fast germination and seedling growth under low temperature is a major breeding objective particularly in direct seeding cropping system in rice growing areas experiencing low temperature stress.

Rice plants are damaged by exposure to cold stress during all stages of plant growth. The optimal temperature range for germination and seedling establishment is 25–35 °C (Chapman and Peterson 1962). However, a number of factors such as varietal difference, duration of cold stress, and physiological stage of the plant are responsible for variation in cold tolerance of rice (Yoshida 1981; Nishiyama 1985). In rice breeding, cold tolerance is usually evaluated at germination, seedling, and reproductive stages. Since field evaluation is challenging, methodologies to evaluate cold tolerance in controlled condition have been developed. Jones and Peterson (1976) developed a slant board test procedure to evaluate seedling vigor under cold stress and noted that shoot length of 15-d old seedling at 18 °C is significantly correlated with seedling vigor in field condition. Correlation between coleoptile length and seedling establishment under low temperature in field condition has been reported (Ogiwara and Terashima 2001). The evaluation of germination index, seedling survival percentage, coleoptile length, radicle length, seedling length, and root length under low temperature has been a common practice in a wide range of studies such as germplasm and cold tolerant near-isogenic lines characterization (Cruz and Milach 2004; Sharifi 2010; Zhou et al. 2012), inheritance studies (Sthapit and Witcombe 1998), and QTL mapping (Fujino et al. 2004).

A number of QTL mapping studies focused on germination under cold stress (Miura et al. 2001; Fujino et al. 2004; Chen et al. 2006; Ranawake et al. 2014) and early seedling cold tolerance (Zhang et al. 2005a; Lou et al. 2007; Liu et al. 2015). In Nipponbare × Kasalath cross, Miura et al. (2001) identified five QTL for germination under low temperature stress on chromosomes 2, 4, 5, and 11 with a total phenotypic variance of 41 %. Nipponbare alleles were beneficial in case of two QTL while Kasalath improved germination under cold stress in rest. Chen et al. (2006) used an indica × japonica cross and identified two QTL for low temperature germination ability on chromosomes 3 and 10. Fujino et al. (2004) identified three QTL on chromosomes 3 and 4 for low temperature germination ability in a cross involving temperate japonica varieties. Of these, the major QTL qLTG3-1 encoding a protein of unknown function was cloned (Fujino et al. 2008).

Ranawake et al. (2014) studied cold tolerance at germination (CTG) and early seedling (CTS) stages in a japonica × indica cross. The cold tolerance QTL in their study were dependent on growth stages. Using seedling survival percentage after cold stress as a criterion, multiple QTL were mapped in several studies (Zhang et al. 2005a; Lou et al. 2007; Liu et al. 2015). In another study, Zhang et al. (2005b) identified 34 QTL for four seedling vigor traits (germination rate, root length, shoot length, and dry weight) at three temperature regimes (25, 20, and 15 °C). Most of these were concentrated in five chromosomal regions with individual QTL contribution ranging from 3 to 16 % of the phenotypic variance. Significant genotype × temperature regime interaction was observed. Among the four seedling vigor traits, shoot length and germination rate were concluded as good predictor for seedling vigor in rice. Combining QTL mapping with micro-array data, Liu et al. (2013) reported a candidate gene (LOC_Os07g22494) that improved cold tolerance at early seedling stage.

Only one QTL mapping study used a recombinant inbred line (RIL) population involving a japonica weedy rice, which was evaluated for cold tolerance at the reproductive stage (Oh et al. 2004). This study demonstrated the utility of weedy rice as potential donor in rice breeding. Although weedy rice belongs to the same genus and species as cultivated rice (Hoagland and Paul 1978), it is noted for its persistence and survival due to its unusual genetic variability and phenotypic plasticity (Oka 1988). The weedy rice infestation is a major challenge for the rice farmers in southern United States and many parts of the world (Webster 2000). Molecular marker-based investigation showed that weedy rices are closer to indica or japonica subspecies of rice rather than the wild species Oryza rufipogon (Suh et al. 1997). But weedy rice accessions of the United States were genetically more diverse and some accessions were found to be closer to O. nivara or O. rufipogon (Vaughan et al. 2001). Weedy rice has many desirable attributes such as rapid seedling growth, higher root mass, deeper root, seedling resistance to pathogen attack (Lee et al. 2000) and tolerance to various biotic and abiotic stresses (Suh et al. 1997, 1999), which can be exploited to boost rice productivity. Unlike wild species of rice, weedy rice hybridizes easily making fertile hybrids and facilitates development of populations for investigating the genetics of useful agronomic and domestication traits.

In this study, we demonstrated that the US weedy rice has enhanced seedling vigor even under cold stress and further identified QTL for cold tolerance and seedling vigor based on seedling attributes in a mapping population involving a US weedy rice accession. Our results suggest that US weedy rice can be an invaluable resource for rice breeding programs to improve both germination and seedling vigor under cold stress.

Materials and methods

Plant materials

A population of 198 RILs in the F7:8 generation was developed from the cross between a medium grain high yielding rice cultivar ‘Bengal’ (Linscombe et al. 1993) and a weedy rice accession PSRR-1 (Subudhi et al. 2012). PSRR-1 was collected from the Rice Research Station at Crowley, LA and was purified by single plant selection for two generations before crossing to develop the mapping population. It has light green leaves, vigorous growth, long auricles and ligules, straw-hulled medium grains, lax open panicles, and pubescent leaves. This weedy rice accession is extremely susceptible to shattering and has a higher intensity of both hull and pericarp dormancy compared to Bengal.

Evaluation of cold tolerance

For each RIL and parents, seeds were treated at 50 °C for 5 days to eliminate residual dormancy. Before initiating the experiment, eight randomly selected RILs and parents were tested for germination. After the germination was tested, seeds of the RIL population and parents were placed in petri dishes lined with a layer of germinating paper (Anchor Paper Co.) with addition of 10 mL of distilled water. The petri dishes were then placed in a basin covered with Saran wrap and transferred to an incubator set at 28 °C for pregermination in darkness. After 2 days of incubation at 28 °C, the pregerminated seeds were transferred to incubators for germination in dark condition under optimum temperature (28 °C) and cold stress (13 °C) for 7 and 14 days, respectively.

A randomized block design with three replications was followed for cold tolerance evaluation. For each line, 20 seeds were used for germination in each replication. Besides germination percentage, observations were recorded on five randomly selected germinating seeds for coleoptile length (CL) and radicle length (RL). For normal condition, the measurements were taken only on the 7th day after incubation. But for cold stress, the measurements were recorded on the 7th and 14th day after incubation. Splitting of the hull by the emerging radicle was used as the criterion for visible germination. The number of seeds germinated in each replication of each RIL and parent was expressed as a percentage. The percent germination was arcsine transformed to improve the normality of distribution for statistical analysis and QTL mapping.

To evaluate the response of parents and individual RIL, cold response index (CRI) was calculated using the formula [CRI = (Phenotypic value after 7 days of incubation at 13 °C)/(Phenotypic value after 7 days of incubation at 28 °C) × 100]. The degree of susceptibility to cold stress at germination stage was ascertained from the CRI values.

All traits were abbreviated as follows: germination percent after 7 days of incubation at 28 °C (Germ7d28C), 13 °C (Germ7d13C), and 14 days of incubation at 13 °C (Germ14d13C); coleoptile length after 7 days of incubation at 28 °C (CL7d28C), 13 °C (CL7d13C), and 14 days of incubation at 13 °C (CL14d13C); radicle length after 7 days of incubation at 28 °C (RL7d28C), 13 °C (RL7d13C) and 14 days of incubation at 13 °C (RL14d13C); CRI for germination (CRI-Germ), CRI for coleoptile length (CRI-CL), CRI for radicle length (CRI-RL).

After evaluating cold tolerance in the laboratory, the germinated seeds were transferred to the greenhouse with 26/18 °C day/night temperature in order to assess the development of the plants in soil. The experiment was conducted in a randomized block design with three replicates. Ten germinated seeds per each RIL were sown in a tray in each replication and five random plants per line were measured for shoot length (StL-GH) and root length (RtL-GH) at14 days after planting in the greenhouse.

Statistical analyses

Analysis of variance (ANOVA) and mean comparison were done using the GLIMMIX procedure. Lines were entered as the fixed effect and the replications were treated as random effect. To improve the normality, data were transformed prior to analysis. Percent germination data were arcsine transformed while the coleoptile and radicle length data were transformed by taking the square root of the value anchored to 0.5. Pearson correlation coefficients among traits were computed based on RIL means using the CORR procedure and broad-sense heritability of each trait was estimated following Holland et al. (2003). All analyses were carried out using SAS (SAS Institute 2011). All histograms were made in Microsoft Excel 2010.

QTL analysis

A linkage map developed in this RIL population (Subudhi et al. 2012) was used for QTL mapping. The linkage map consisted of 212 simple sequence repeat (SSR) markers and a morphological marker Rc (the pericarp color) with a total map distance of 1410 cM and average marker interval of 6.6 cM. Both single marker analysis and composite interval mapping (CIM) were performed using QTL Cartographer version 2.5 (Wang et al. 2011). In the CIM procedure, a forward–backward regression procedure with 20 cofactors was followed with walk in speed of 1.0 cM for detection of QTL. Logarithm of odds (LOD) score of 2.5 was used as the threshold for declaring significance of the QTL. Since QTL identified using data taken after 14 days of exposure at 13 °C were same as those from 7 days at 13 °C, those data were not provided. The QTL were named following McCouch et al. (1997). For example, the QTL located on chromosome 3 for germination percentage after 7 days of exposure to 28 °C was named as qGerm7d 28C-3.

Results

Variation in early seedling vigor and cold tolerance response among parents and RILs

Analysis of variance revealed significant differences with respect to all traits in the RIL population except RL7d28C. Descriptive statistics with respect to germination and early seedling vigor traits under both normal and cold stress were presented in Table 1. Bengal and PSRR-1 did not differ in the germination rate 7 days after incubation at 28 °C, but there were significant differences in coleoptile length and radicle length (Fig. 1). For both traits, weedy rice accession PSRR-1 showed better performance compared with Bengal.

Table 1 Descriptive statistics for cold tolerance-related traits during germination and early seedling stage in Bengal × PSRR-1 RIL mapping population of rice
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Fig. 1
figure 1

Germination of parents under optimum temperature and cold stress. Pictures were taken 7 days after incubation at 28 °C (top) and 13 °C (middle), and 14 days after incubation at 13 °C (bottom)

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Low temperature stress reduced germination percentage significantly in ‘Bengal’ after 7 and 14 days. However, PSRR-1 maintained the same germination rate under cold stress like the optimum condition. At both time points, germination remained around 70 % in Bengal. Cold stress seriously damaged the coleoptile and radicle growth. But PSRR-1 grew significantly faster compared with Bengal. To compare the performance of both parents under cold stress relative to optimum condition, cold response index was calculated. For all three traits, PSRR-1 was better than Bengal. To observe the impact of cold stress at early seedling stage, seedlings were planted in the greenhouse under normal temperature for 14 days. PSRR-1 had significantly greater shoot length compared to Bengal, whereas there was no difference in root length.

There was a wide range of variability in the population. For the traits, Germ7d28C, Germ7d13C, and Germ14d13C, distribution was skewed (Fig. 2). The distribution for coleoptile and radicle length at both optimum and low temperatures was normal (Fig. 3). The distribution for CRI (CL) was normal but the CRI for other two traits was a little skewed (Fig. 4). The traits, StL-GH and RtL-GH, were normally distributed with many of the RILs falling outside of the parental range indicating transgressive segregation (Fig. 5). Mean values of the RIL population were lower than both parents for Germ7d28C, Germ7d13C, CL7d28C, and RL7d28C but higher than the parent with higher mean for CL7d13C, CRI (CL), and CRI (RL) and similar or within the parental range in the rest.

Fig. 2
figure 2

Frequency distribution of germination% under cold stress in the RIL population of the cross Bengal × PSRR-1. Mean values for parents and RIL population are marked by arrows. B, P, and R represent for Bengal, PSRR-1, and RIL population, respectively. Germ7d28C, Arcsine transformed values of germination% after 7 days at 28 °C; Germ7d13C, Arcsine transformed values of germination% after 7 days at 13 °C; Germ14d13C, Arcsine transformed values of germination% after 14 days at 13 °C

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Fig. 3
figure 3

Frequency distribution of coleoptile length and radicle length under cold stress in the RIL population of the cross Bengal × PSRR-1. Parental means are marked by arrows. B, P, and R represent mean values for Bengal, PSRR-1, and RIL population, respectively. CL7d28C, Coleoptile length after 7 days at 28 °C; RL7d28C, Radicle length after 7 days at 28 °C; CL7d13C, Coleoptile length after 7 days at 13 °C; RL7d13C, Radicle length after 7 days at 13 °C; CL14d13C, Coleoptile length after 14 days at 13 °C; RL14d13C, Radicle length after 14 days at 13 °C

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Fig. 4
figure 4

Frequency distribution of cold response indices in RIL population of the cross Bengal × PSRR-1. Mean values for parents and RIL population are marked by arrows. B, P, and R represent for Bengal, PSRR-1, and RIL population, respectively. Cold response indices were calculated as [(trait mean at 13 °C/trait mean at 28 °C) × 100]

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Fig. 5
figure 5

Frequency distribution of shoot length and root length 14 days after transplanting in greenhouse in RIL population of the cross Bengal × PSRR-1. The germinated seeds were transferred to greenhouse after the cold tolerance evaluation in the laboratory. Mean values for parents and RIL population are marked by arrows. B, P, and R represent for Bengal, PSRR-1, and RIL population, respectively. StL-GH, shoot length in greenhouse experiment; RtL-GH, root length in greenhouse experiment

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Broad sense heritability was moderate to high for Germ7d28C, Germ7d13C, Germ14d13C, CL7d28C, CRI (Germ), CRI (CL), and RL7d13C, and was low for CL7d13C, RL7d28C, CRI (RL), StL-GH, and RtL-GH.

Correlations among traits

As shown in Table 2, the phenotypic correlations among all germination and early vigor traits were all positive and highly significant (P < 0.001). The only negative and significant correlation was observed between CRI-RL and RL7d28C. The germination percentage under optimum temperature was highly correlated to traits measured under both optimum and low temperature stress, but the radicle length under optimum condition or root length under greenhouse was either not correlated with many of these traits or the strength of most correlations was low. The cold response index for coleoptile length and radicle length did not show correlation with the seedling traits measured in greenhouse after exposure to cold stress.

Table 2 Pearson correlation coefficients between the early seedling stage cold tolerance and seedling vigor traits in the RIL mapping population of rice cross Bengal × PSRR-1
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Quantitative trait loci for germination ability and seedling growth under cold stress

Scanning of the whole genome detected 49 QTL for eleven traits distributed along ten chromosomes under both control and low temperature stress environments (Table 3; Fig. 6). Thirty QTL were clustered within six regions of five chromosomes 1, 3, 8, 11, and 12. The number of QTL varied between one and nine per trait and each QTL contributed 3.5–12.7 % of the total phenotypic variation. The weedy PSRR-1 alleles increased the trait means in 31 QTL and Bengal alleles were favorable in the rest.

Table 3 Chromosome location, additive effects, direction of phenotypic effect, and estimate phenotypic variance of the putative QTL associated with early seedling stage cold tolerance and seedling vigor detected in the RIL population of the cross Bengal × PSRR-1 using composite interval mapping procedure
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Fig. 6
figure 6

Chromosomal location of QTL for traits related to early seedling stage cold tolerance and seedling vigor in the RIL population developed from the cross Bengal × PSRR-1 (Subudhi et al. 2012). QTL are shown on the left side of each chromosome. Bars with upward pointing arrows indicate increasing effect on trait mean by Bengal allele and bars with downward pointing arrows indicate PSRR allele increasing the trait mean. Germ7d28C, Arcsine transformed values of germination% after 7 days at 28 °C; Germ7d13C, Arcsine transformed values of germination% after 7 days at 13 °C; CRI-Germ, cold response index for germination; CL7d28C, Coleoptile length after 7 days at 28 °C; CL7d13C, Coleoptile length after 7 days at 13 °C; CRI-CL, cold response index for coleoptile length; RL7d28C, Radicle length after 7 days at 28 °C; RL7d13C, Radicle length after 7 days at 13 °C; CRI-RL, cold response index for radicle length; StL-GH, shoot length in greenhouse experiment; RtL-GH, root length in greenhouse experiment

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Further examination of QTL results revealed the following points. Only one QTL was detected for Germ7d28C with Bengal allele improving germination percentage, but three QTL were detected under cold stress including the one for Germ7d28C. For the two QTL, PSRR-1 allele improved germination under cold stress. For the cold response index, two of the four QTL were same as the QTL for Germ7d13C and two were new.

For traits, CL7d28C, CL7d13C, and CRI-CL, 6, 8, and 9 QTL were detected, respectively (Table 3; Fig. 6). Only one QTL on chromosome 2 was common under both optimum and cold temperature. Five QTL located on chromosomes 1, 3, 8, and 12 were identical with respect to the direction of additive effect between CRI-CL and CL7d13C. Only one major QTL from PSRR-1 accounting for a phenotypic variation of 11 % was located on chromosome 8. For RL7d28C and RL7d13C, three QTL were detected for each trait, but six QTL were identified for CRI-RL. In case of two of the 3 QTL for CL7d28C, Bengal allele was desirable. There were two common QTL on identical position for these traits. None of these QTL explained phenotypic variation greater than 10 %. There were three QTL each identified for StL-GH and RtL-GH and PSRR-1 contributed the allele for cold tolerance in case of two QTL. There was no overlapping of QTL between them. But there was one major QTL on chromosome 11 explaining 11 % of phenotypic variation and desirable allele was from PSRR-1.

Based on the radicle length and coleoptile length under normal condition of growth, PSRR-1 showed improved seedling vigor compared with Bengal. But the QTL mapping results for both traits under optimum environments revealed that both parents had genes or QTL, which can improve seedling vigor. For example, there were two QTL each for CL7d28C and RL7d28C with Bengal allele providing the alleles with positive effects. Other traits measured under cold stress followed a similar trend with both parents contributing alleles to improve germination ability and early seedling vigor under low temperature stress.

Discussion

Low temperature in temperate and high altitude areas of the tropical regions is a major hindrance to rice cultivation. It has a detrimental effect on germination, seedling growth, and reproductive success by interfering with the metabolism (Zhang et al. 2014a, b). Since tolerance to low temperature at a particular stage of crop growth is not correlated to cold tolerance at other developmental stages (Kaw and Khush 1985; Zhou et al. 2012), QTL studies had been conducted to investigate cold tolerance at various growth and developmental stages such as germination stage (Miura et al. 2001; Fujino et al. 2004), seedling stage (Kim et al. 2014; Zhang et al. 2014a, b; Liu et al. 2015), vegetative stage (Andaya and Mackill 2002), and booting stage (Andaya and Mackill 2003; Oh et al. 2004). In this study, we focused on germination ability and early seedling growth under cold stress, which are important factors for uniform stand establishment in rice growing areas of southern USA, where cold temperature prevents germination in dry seeded rice.

There was no difference in germination rate under optimum temperature. Therefore, it was obvious that we detected only one QTL from the cultivated rice suggesting little genetic difference between both parents with respect to germination ability at optimum temperature. However, there was a strong contrast between both parents for germination ability under cold stress, which was supported by detection of four QTL on chromosomes 1, 7, 11, and 12 controlling this trait and PSRR-1 alleles in all cases were superior to Bengal (Table 3). The reduction in coleoptile length and radicle length was higher compared to observation in Japanese rice germplasm (Bosetti et al. 2012).

Since PSRR-1 was superior to Bengal with respect to the coleoptile length and radicle length under optimal temperature regime (Table 1), it provided an opportunity to identify the genomic regions responsible for such attributes related to seedling vigor. There was no colocalisation of the QTL for coleoptile length and radicle length indicating different genes responsible for these traits. The QTL alleles from both parents contributed to the improvement of seedling vigor under optimum temperature.

Comparison of QTL positions on the rice genome with those detected in prior studies provided information about the QTL consistency despite the differences in marker types, the genetic materials, and screening methodology. Miura et al. (2001) reported five QTL on chromosomes 2, 4, 5, and 11 controlling germination ability under cold stress. Three of these QTL on chromosomes 2, 5, and 11 were located in similar positions in our study. Fujino et al. (2004) identified 3 QTL on chromosomes 3 and 4 with one major QTL qLTG-3-1 explaining 35 % of phenotypic variation, which was later cloned (Fujino et al. 2008). However, we did not detect any QTL on corresponding locations of both chromosomes. Baruah et al. (2009) reported five QTL for cold tolerance at the plumule and seedling stage in a cross between a japonica rice A58 and an wild rice accession W107 (O. rufipogon). The QTL on chromosome 11, which was consistent at plumule and seedling stages, also overlapped with the same genomic region harboring several QTL for cold tolerance attributes in our study (Fig. 6). Few other studies reported 2-5 QTL or genomic regions controlling these attributes (Chen et al. 2006; Zhang et al. 2005b; Ranawake et al. 2014). There was no overlapping of QTL detected in our study with those identified by Chen et al. (2006). Three QTL on chromosomes 6 and 7 for germination ability under cold stress and two QTL on chromosomes 6 and 11 for cold tolerance at seedling stage (Ranawake et al. 2014) coincided with our study. Several studies reported QTL for cold tolerance traits such as seedling vigor (Zhang et al. 2005a; Baruah et al. 2009), tolerance to seedling stage necrosis (Andaya and Mackill 2003), and seedling stage cold tolerance (Kim et al. 2014) in the similar region on chromosome 11. Considering all these reports, it is clear that this chromosome 11 location might be a hot spot for genes responsible for cold tolerance at germination and seedling stages. A candidate gene, ORF LOC_Os11g37720 (Duf6 gene), co-segregating with seedling cold tolerance was reported (Kim et al. 2014). Further exploration of this region using the introgression line PSRR-1 (Subudhi et al. 2015) should lead to cloning of the genes responsible for various component traits of cold tolerance.

Mapping of seedling vigor, which was assessed in both laboratory and greenhouse condition revealed that genes controlling seedling vigor under cold stress were different from those under normal temperature (Fig. 6). When QTL results for all traits were considered in totality, we observed that there were six clusters of QTL for multiple seedling vigor and germination traits under cold stress on chromosomes 1, 3, 8, 11, and 12. For the two clusters on chromosomes 3 and 12, positive alleles for all cold tolerance traits were from ‘Bengal’, whereas weedy rice alleles improved cold tolerance in the remaining 4 clusters. Strong correlations observed among the traits (Table 2) were consistent with QTL mapping results because the majority of QTL for both germination ability and seedling vigor traits were colocalized in few chromosomal regions with the same parental allele either decreasing or increasing the trait mean (Fig. 6; Table 3). It is interesting to note that most of the congruent QTL were not localized in the QTL clusters detected in this study with the exception of that on chromosome 11. It appears that these QTL are novel compared with the earlier reports (Miura et al. 2001; Fujino et al. 2004; Zhang et al. 2005b; Chen et al. 2006; Ranawake et al. 2014). Most of these studies used indica × japonica cross with the exception of Fujino et al. (2004), who used the population developed from the cross between two japonica varieties. Unlike the above studies, the mapping population used in our study involved a japonica variety and a weedy rice accession. Therefore the discrepancy in QTL detection could be due to the differences in the genetic background of the plant materials. Zhang et al. (2005b) reported five genomic regions where QTL for multiple traits were evaluated to assess seedling vigor. Each cluster was designated as a putative QTL, which could be either cluster of linked loci or single locus with pleiotropic effects. Another finding was that two StL-GH QTL and one RtL-GH QTL were placed in these clusters along with other seedling and germination attributes, which suggest that these traits could be used as reliable indicators to evaluate seedling vigor under cold stress (Zhang et al. 2005b).

The weedy rice accession PSRR-1 was collected from the rice field in Louisiana, USA, where cold stress is common during the rice cropping season. High level of seed germination ability under cold stress in this weedy rice accession might be due to strong selection pressure for cold tolerance and early seedling vigor (Mackill and Lei 1997; Baruah et al. 2009). Weedy rice populations from different geographic location of China have been reported to evolve rapidly with respect to their germination response due to genetic differentiation (Chen et al. 2004; Xia et al. 2011). Despite many weedy attributes, weedy rice could be an important resource for genetic improvement of crop plants like other wild relatives (Lu and Ellstrand 2014). We showed that the four QTL clusters on chromosomes 1, 8, 11, and 12, where weedy rice alleles were beneficial, would be useful for marker-assisted selection to introduce a high level of cold tolerance and seedling vigor to rice cultivars grown in the USA. Since we observed transgressive variation for both improved germination and vigor under cold stress in the mapping population, it is likely that these QTL alleles from weedy rice in combination with the favorable alleles of the cultivated rice would result in rice varieties with improved cold tolerance. Consequently, cloning of these QTL using the introgression lines of this weedy rice accession developed in a cultivated background (Subudhi et al. 2015) should aid in the precise transfer of the cold tolerance attributes from the weed rice.