SNP Loci and Favorable Haplotype Mining for Alkalinity Tolerance in the Rice Bud Stage

Author:

Zhou Zhenzhen1,Du Mingyu1,Liu Zhengbo1,Chang Yingping1,Xiong Mengyuan1,Sun Hao1,Cheng Xianping1,Zhang Yanan1,Sun Jinghan1,Wang Rui1,Zhang Mengyuan1,Li Xinru1,Li Min1,Zhang Chaopu1,Liu Erbao1ORCID

Affiliation:

1. College of Agronomy, Anhui Agricultural University, Hefei 230036, China

Abstract

The mining of favorable SNP loci and haplotypes is of great significance for the further cloning and molecular-assisted breeding of alkalinity-tolerance genes in rice. To improve the utilization rate of saline–alkaline lands and the yield of rice, we used the 1,322,884 SNPs obtained from the sequencing 173 of rice accessions in this study. Alkalinity-tolerance-related traits, including the germination energy (GE), germination rate (GR), seedling length (SL), root length (RL), relative alkaline damage rate (RADR) of the GERADR of the GR, RADR of the SL and RADR of the RL, were evaluated in 2019 and 2020 and revealed abundant phenotypes in the studied population. A genome-wide association analysis detected 10 quantitative trait loci (QTLs) related to alkalinity tolerance. In addition, a transcriptome sequencing analysis of the alkalinity-tolerant rice variety ‘Yuedao 9’ and the alkali-sensitive rice variety ‘Tijin’ under alkalinity stress and control conditions was performed. Three candidate genes that were predicted to be related to alkalinity tolerance in rice, namely LOC_Os06g06600, LOC_Os011g44680 and LOC_Os011g44600, were screened based on gene annotation, coding sequences and haplotype analysis. The results of this study provide important genetic information for the molecular improvement of rice.

Funder

National Natural Science Foundation of China

Talent Project of Anhui Agricultural University

Natural Science Foundation of Anhui Province

Natural Science Foundation of Anhui Universities

Natural Science Research Project of Colleges and Universities in Anhui Province

Key Research and Development Program of Anhui Province

Publisher

MDPI AG

Subject

Agronomy and Crop Science

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