New alleles for chlorophyll content and stay-green traits revealed by a genome wide association study in rice (Oryza sativa)

Scientific Reports
Yan ZhaoJinjie Li

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...Continue Reading

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Citations

Nov 24, 2019·International Journal of Molecular Sciences·Nasrein Mohamed KamalHisashi Tsujimoto
Mar 7, 2020·International Journal of Molecular Sciences·Kyu-Chan ShimSang-Nag Ahn
Oct 17, 2019·Plants·Sofia Bengoa LuoniRuth Heinz
Jan 26, 2021·Frontiers in Plant Science·Sophie JasinskiFabien Chardon
Apr 6, 2021·The Plant Genome·Jacques M FayeGeoffrey P Morris
May 1, 2021·International Journal of Molecular Sciences·Sichul Lee, Celine Masclaux-Daubresse

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Methods Mentioned

BETA
dissection
genotyping
two-hybrid

Software Mentioned

R package “ LD heatmap ”
cytoscape
MEGA
ANVOA
in
PLINK
TASSEL
GAPIT
ClueGO
house Perl script

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