Genome-wide association mapping and gene expression analysis reveal candidate genes for grain chalkiness in rice
文献类型： 外文期刊
作者： Huo, Xing 1 ; Wang, Jian 1 ; Chen, Luo 1 ; Fu, Hua 1 ; Yang, Tifeng 1 ; Dong, Jingfang 1 ; Ma, Yamei 1 ; Zhou, Lian 1 ; Chen, Jiansong 1 ; Liu, Dilin 1 ; Liu, Bin 1 ; Zhao, Junliang 1 ; Zhang, Shaohong 1 ; Yang, Wu 1 ;
作者机构： 1.Guangdong Acad Agr Sci, Rice Res Inst, Guangdong Key Lab New Technol Rice Breeding, Guangdong Rice Engn Lab,Key Lab Genet & Breeding H, Guangzhou, Peoples R China
关键词： rice; grain chalkiness; genome-wide association study; quantitative trait loci (QTL); candidate gene
期刊名称：FRONTIERS IN PLANT SCIENCE （ 2022影响因子：5.6； 五年影响因子：6.8 ）
ISSN： 1664-462X
年卷期： 2023 年 14 卷
收录情况： SCI
摘要： Grain chalkiness is the main factor determining the market value of rice. Reducing chalkiness is an important breeding goal for genetic improvement of high quality rice. Identification of QTLs or genes controlling chalkiness is the prerequisite for molecular breeding in rice. Here, we conducted a genome-wide association study to identify QTLs associated with grain chalkiness including percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) in 450 rice accessions consisting of 300 indica and 150 japonica rice in two environments. A total of 34 QTLs were identified, including 14 QTLs for PGWC and 20 QTLs for DEC. Among them, seven QTLs were commonly identified in two environments, and eight QTLs were simultaneously related to two traits. Based on the haplotype analysis, LD decay analysis, RNA-sequencing, qRT-PCR confirmation and haplotype comparisons, four genes (LOC_Os10g36170, LOC_Os10g36260, LOC_Os10g36340 and LOC_Os10g36610) were considered as the candidate genes for qDEC-10c(1w,2wj), which could be identified in both environments and had the most significant p-value among the newly identified QTLs. These results provided new insight into the genetic basis of grain chalkiness and gene resources for improving quality by molecular breeding in rice.
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