Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping.

BACKGROUND: Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method. RESULTS: Among the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (r GCC-FSC = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC. CONCLUSION: Not every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype.

Fine Mapping and Candidate Gene Analysis of qSTL3, a Stigma Length-Conditioning Locus in Rice (Oryza sativa L.).

The efficiency of hybrid seed production can be improved by increasing the percentage of exserted stigma, which is closely related to the stigma length in rice. In the chromosome segment substitute line (CSSL) population derived from Nipponbare (recipient) and Kasalath (donor), a single CSSL (SSSL14) was found to show a longer stigma length than that of Nipponbare. The difference in stigma length between Nipponbare and SSSL14 was controlled by one locus (qSTL3). Using 7,917 individuals from the SSSL14/Nipponbare F2 population, the qSTL3 locus was delimited to a 19.8-kb region in the middle of the short arm of chromosome 3. Within the 19.8-kb chromosome region, three annotated genes (LOC_Os03g14850, LOC_Os03g14860 and LOC_Os03g14880) were found in the rice genome annotation database. According to gene sequence alignments in LOC_Os03g14850, a transition of G (Nipponbare) to A (Kasalath) was detected at the 474-bp site in CDS. The transition created a stop codon, leading to a deletion of 28 amino acids in the deduced peptide sequence in Kasalath. A T-DNA insertion mutant (05Z11CN28) of LOC_Os03g14850 showed a longer stigma length than that of wild type (Zhonghua 11), validating that LOC_Os03g14850 is the gene controlling stigma length. However, the Kasalath allele of LOC_Os03g14850 is unique because all of the alleles were the same as that of Nipponbare at the 474-bp site in the CDS of LOC_Os03g14850 among the investigated accessions with different stigma lengths. A gene-specific InDel marker LQ30 was developed for improving stigma length during rice hybrid breeding by marker-assisted selection.

Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.).

Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker-trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.