Exploring the genetic basis of pre-harvest sprouting in rice through a genome-wide association study-based haplotype analysis  

作　　者：Myeong-Hyeon Min Aye Aye Khaing Sang-Ho Chu Bhagwat Nawade Yong-Jin Park 

机构地区：[1]Department of Plant Resources,College of Industrial Sciences,Kongju National University,Yesan 32439,Republic of Korea [2]Department of Agronomy,Yezin Agricultural University,Nay Pyi Taw 15013,Myanmar

出　　处：《Journal of Integrative Agriculture》2024年第8期2525-2540,共16页农业科学学报（英文版）

基　　金：supported by the National Research Foundation of Korea(NRF)grants funded by the Ministry of Science and Information and Communication Technology(MSIT),Republic of Korea(NRF2022R1A4A1030348 and 2023R1A2C1004432);the Korea Institute of Planning and Evaluation for Technology in Food,Agriculture and Forestry(IPET)through the Digital Breeding Transformation Technology Development Program,funded by the Ministry of Agriculture,Food and Rural Affairs(MAFRA),Republic of Korea(322060031HD020);the Cooperative Research Program for Agriculture Science and Technology Development,Rural Development Administration,Republic of Korea(RS-2023-00222739)。

摘　　要：Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identify novel PHS-associated haplotypes.An assessment of 127 cultivated accessions for panicle germination(PHS)and detached grain germination(germination rate of detached grains at the 14th day(D14))revealed considerable phenotypic variation among rice ecotypes.GWAS analysis identified 91 significant signals at–log10(P-value)>5,including 15SNPs for PHS and 76 SNPs for D14.A subsequent linkage disequilibrium(LD)block-based GWAS analysis detected 227 significant SNPs for both traits,consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes.Further haplotype analysis identified 32 haplotypes,with 10 specific to cultivated accessions,19 specific to the wild type,and three shared between them.A phenotypic assessment of major haplotypes revealed significant differences between resistant(Hap1 and Hap2)and susceptible haplotypes(Hap5,Hap27,and Hap28),distinguished by a G/A SNP within a novel gene,Os04g0545200.The identified haplotypes offer promising prospects for haplotypebased breeding aimed at enhancing PHS resistance in rice.

关 键 词：RICE PHS DORMANCY GERMINATION GWAS HAPLOTYPE abiotic stress 

分 类 号：S511[农业科学—作物学]