Haplotype Analysis and Marker Development of Five Salt-tolerant-related Genes in Rice ( L.)

Overview

Journal Front Plant Sci

Date 2023 Sep 20

PMID 37727858

Authors

Pingbo Li

Zhen Li

Xu Liu

Hua Zhang

Shuyong Zhang

Fang Liu

Nana Li

Yongyi Yang

Kun Xie

Hanfeng Ding

Fangyin Yao

Affiliations

Soon will be listed here.

Abstract

Salinity stress is a great threat to the growth and productivity of crops, and development of salt-tolerant crops is of great necessity to ensure food security. Although a few genes with natural variations that confer salt tolerance at germination and seedling stage in rice have been cloned, effective intragenic markers for these genes are awaited to be developed, which hinder the use of these genes in genetic improvement of salt tolerance in rice. In this study, we first performed haplotype analysis of five rice salt-tolerant-related genes using 38 rice accessions with reference genome and 4,726 rice germplasm accessions with imputed genotypes and classified main haplotype groups and haplotypes. Subsequently, we identified unique variations for elite haplotypes reported in previous studies and developed 11 effective intragenic makers. Finally, we conducted genotyping of 533 of the 4,726 rice accessions from worldwide and 70 approved temperate / cultivars in China using the developed markers. These results could provide effective donors and markers of salt-tolerant-related genes and thus could be of great use in genetic improvement of salt tolerance in rice.

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