| Rapid and uniform seed germination is one of the important agronomic traits and critical for direct seeding in rice. The Asian cultivated rice (O. sativa L.) consists of two subspecies, indica (O. sativa L. ssp. indica) and japonica (O. sativa L. ssp. japonica). Generally, indica cultivars geminate faster than japonica. Here, we developed a set of chromosomal segment substitution lines (CSSL) by backcrossing and marker-assisted selection in which the japonica Nipponbare was the donor parent, and the recurrent parent was the indica ’Zhenshan97B’(ZS97B). Each line contains a substituted Nipponbare donor segment of a particular chromosomal region within the uniform genetic background of the ZS97B, and all the substitution segments together cover the entire Nipponbare genome. We surveyed genetic bases of germination rate using this set of143CSSLs, validated and finely mapped a major QTL (qGR2) for germination rate. The main results are as follows:1. The differences in germination rate existed stably between ZS97B and Nipponbare at various genmination temperature conditions (13℃,18℃,23℃and28℃). Besides the two parents (ZS97B and Nipponbare), the other42cultivars also showed great variation in germination rate under23℃at2days after imbibition. On average, the germination rate of indica cultivars was5.8times faster than that in the japonica.2. Four QTL (qGR2, qGR5, qGR6and qGR10) were identified for germination rate in the CSSL population, of which all the japonica alleles decreased the germination rate.3. Using a F2population derived from a CSSL (CSSL29) that contains the target substitution region on chromosome2and ZS97B, qGR2was confirmed as a major QTL explained24.3%of phenotypic variance, and located in the interval of RM12532-RM12544. A large segregation population comprised2,720individuals was further generated by selfing a single F2individual heterozygous at the qGR2region. Twenty-three informative recombinants were identified with8markers in the region, and grouped into six genotype classes according to the positions of recombinant points and allelic composition. Multiple comparisons of the germination rate among the six genotypes and the control (ZS97B) narrowed qGR2down to a genomic region between RM12530and RM423, a segment about60-kb in length. The position of the QTL underlying germination rate was narrowed down even further to a10.4-kb length defined by markers MC04and RM423by analyzing more SNP markers in the interval. This small region is on a single bacterial artificial chromosome clone and contains three predicted genes, namely Loc_Os02g07410, Loc_Os02g07420, and Loc_Os02g07430(OsMADS29).4. Germination rate was significantly and positively correlated with protein content, but not with seed shape, amylose content, and1,000-grain weight in the143CSSL.5. Expression analysis by RT-PCR revealed different expression patterns of the gene OsMADS29in ZS97B and CSSL29during seed germination. These differences in the time of expression were highly consistent with that time taken for radicle protrusion in ZS97B and CSSL29.6. There were significant differences in amylose content, protein content, gel consistency, and grain chalkiness between ZS97B and Nipponpare. We detected36QTLs for six grain quality traits. Several major QTLs co-located with the known quality genes such as Wx, alk, of which Nipponbare alleles could improve the grain quality of ZS97B.7. Association analysis showed that the grain quality including protein content, gel consistency, grain chalkiness are associated with heading date in the143CSSLs, indicating that these grain quality traits in rice is highly influenced by environment.8. We have constructed seven CSSLs each containing at least one favorable gene from Nippobare for grain quality. The testcrossing hybrids between the CSSL and Minghui63, an elite restorer line, showed a remarkable improvement in grain quality, suggesting a potential way to improve the grain quality of ZS97B and its hybrids. |
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