Abstract
Higher chlorophyll content (CC) and strong stay-green (SG) traits are conducive for improvement of photosynthetic efficiency in plants. Exploration of natural elite alleles for CC and SG, and highly resolved gene haplotypes are beneficial to rational design of breeding for high-photosynthetic efficiency. Phenotypic analysis of 368 rice accessions showed no significant correlation between CC and SG, and higher CC and stronger SG in japonica than in indica. Genome-wide association studies of six indices for CC and SG identified a large number of association signals, among which 14 were identified as pleiotropic regions for CC and SG. Twenty-five known genes and pleiotropic candidate gene OsSG1 accounted for natural variation in CC and SG. Further analysis indicated that 20 large-effect, non-synonymous SNPs within six known genes around GWAS signals and three SNPs in the promoter of OsSG1 could be functional causing significant phenotypic differences between alleles. Superior haplotypes were identified based on these potentially functional SNPs. Population analyses of 368 cultivated accessions and 446 wild accessions based on SNPs within genes for CC and SG suggested that these genes had been subjected to strong positive selection in japonica in the process of spreading from its subtropical origin to the North China temperate zone. Our studies point to important genes that account for natural variation and provide superior haplotypes of possible functional SNPs that will be beneficial in breeding for high-photosynthetic efficiency in rice.
Highlights
Higher chlorophyll content (CC) and strong stay-green (SG) traits are conducive for improvement of photosynthetic efficiency in plants
The genetic architecture of natural variation in rice CC was investigated through genome-wide association studies (GWAS), and genes Ghd[7] and NAL were found to be associated with CC25
Large variations were observed in the whole population among CC indices SFH and three upper leaves at heading (TSH), SG indices ADSF and RDSF, and accumulation of chlorophyll (ACC) indices CSF and TCS (Fig. S2)
Summary
Higher chlorophyll content (CC) and strong stay-green (SG) traits are conducive for improvement of photosynthetic efficiency in plants. Our studies point to important genes that account for natural variation and provide superior haplotypes of possible functional SNPs that will be beneficial in breeding for high-photosynthetic efficiency in rice. Rich genetic diversity and clear subspecies and population differentiation are established characteristics of Asian cultivated rice[20,21,22,23,24] These natural variations underlie adaptability to different light and temperature conditions that range from tropical to temperate zones, and lay a genetic basis for breeding adapted varieties with high and stable yields. Given that molecular breeding relies on precise genetic dissection of agronomic traits and high-resolution chromosome haplotypes[26], further identification of elite alleles underlying CC and SG will be beneficial in gaining insights into the molecular basis of variation in CC and SG and in breeding photosynthetically efficient varieties. The results provide insight into how domestication has affected CC and SG genes as well as information that may be useful for future molecular applications of these genes in breeding for high photosynthetic efficiency
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