Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.)

Abstract

Quantitative trait loci (QTLs) controlling seed longevity in rice were identified using 98 backcross inbred lines (BILs) derived from a cross between a japonica variety Nipponbare and an indica variety Kasalath. Seeds of each BIL were kept for 12 months at 30 degrees C in dry conditions to promote loss of viability. To measure seed longevity, we performed an additional aging-processing treatment for 2 months at 30 degrees C maintaining seeds at 15% moisture content. We measured the germination percent of these treated seeds at 25 degrees C for 7 days as the degree of seed longevity. The germination of BILs ranged from 0 to 100% with continuous variation. Three putative QTLs for seed longevity, qLG-2, qLG-4 and qLG-9, were detected on chromosome 2, 4 and 9, respectively. Kasalath alleles increased the seed longevity at these QTLs. The QTL with the largest effect, qLG-9, explained 59.5% of total phenotypic variation in BILs. The other two QTLs, qLG-2 and qLG-4, explained 13.4 and 11.6% of the total phenotypic variation, respectively. We also verified the effect of the Kasalath allele of qLG-9 using chromosome segment substitution lines. Furthermore, QTLs for seed dormancy were identified on chromosomes 1, 3, 5, 7 and 11. Based on the comparison of the chromosomal location of QTLs for seed longevity and seed dormancy, these traits seem to be controlled by different genetic factors.

Genetic mapping within the wheat D genome reveals QTL for germination, seed vigour and longevity, and early seedling growth

“…Thus the use of seed lots from different reproduction years in the DILs dormancy study and the present study might account for the observed differences in the locations of dormancy and longevity QTL. However, studies on the relationship between these traits in rice (Miura et al 2002) andA. thaliana (Clerxk et al 2004) using seed produced in the same year and under the same conditions to reduce the environmental effects support independent genetic control of these traits.…”

“…Seed longevity is determined by a number of environmental and genetic factors, and while many attempts have been made to optimize storage conditions (Ellis et al 1982(Ellis et al , 1993Barzali et al 2005), its inheritance and genetic control is poorly researched. Both inter-and intraspecific variability have been demonstrated in model and crop plant species (Walters et al 2005), and genes responsible for differences in seed longevity have been identified in A. thaliana (Clerkx et al 2004), cabbage (Bettey et al 2000), rice (Miura et al 2002;Sasaki et al 2005;Zeng et al 2006;Xue et al 2008), and barley (Nagel et al 2009). In rice, a series of mapping populations revealed QTL for seed longevity/storability mapping to seven chromosomes; however, only those on chromosome 9 were consistently identified.…”

“…(Bettey et al 2000), rice (Cui et al 2002), barley (Edney and Mather 2004), sunflower (Al Chaarani et al 2005) and wheat (Landjeva et al 2008). Genomic regions harbouring QTL associated with seed longevity have been identified in rice (Miura et al 2002;Sasaki et al 2005;Zeng et al 2006;Xue et al 2008), Arabidopsis thaliana (Clerkx et al 2004) and barley (Nagel et al 2009). …”

QTL analysis of seed dormancy in rice (Oryza sativa L.)

“…Recently many QTLs affecting SD and PHS tolerance have been identified in various plant species such as barley (Oberthur et al, 1995;Larson et al, 1996;Han et al, 1996;Li et al, 2004;Thomas et al, 1996), wheat (Anderson et al, 1993;Flintham et al, 2002;Kato et al, 2001;Roy et al, 1999;Zanetti et al, 2000), Arabidopsis (van der Schaar et al, 1997), and rice (Wan et al, 1997;Lin et al, 1998;Cai & Morishima, 2000;Dong et al, 2003;Miura et al, 2002). These studies have identified various genetic loci for SD and PHS, which in part reflect the different samplings from the available gene pools and indicate that many genes are involved in SD and PHS.…”

Mapping of quantitative trait loci associated with ultraviolet-B resistance in rice (Oryza sativa L.)

“…In rice, molecular genetic maps and markers have facilitated the identification of QTLs for the trait of interest (McCouch and Doerge 1995;Yano and Sasaki 1997). Furthermore, DNA marker-assisted selection has made it possible to develop near-isogenic lines and chromosome segment substitution lines for QTL regions affecting agronomic and physiological traits including resistance to environmental stress (Lin et al 1998;Lin et al 2000;Miura 2001Miura , 2002Ma et al 2002). In addition, molecular cloning of genes at QTLs has been achieved by a mapbased strategy (reviewed by Yano 2001).…”