A Genome-Wide Association Study Coupled With a Transcriptomic Analysis Reveals the Genetic Loci and Candidate Genes Governing the Flowering Time in Alfalfa (Medicago sativa L.)

Fei He; Fan Zhang; Xueqian Jiang; Ruicai Long; Zhen Wang; Yishi Chen; Mingna Li; Ting Gao; Tianhui Yang; Chuan Wang; Junmei Kang; Lin Chen; Qingchuan Yang

doi:10.3389/fpls.2022.913947

A Genome-Wide Association Study Coupled With a Transcriptomic Analysis Reveals the Genetic Loci and Candidate Genes Governing the Flowering Time in Alfalfa (Medicago sativa L.)

Front Plant Sci. 2022 Jul 11:13:913947. doi: 10.3389/fpls.2022.913947. eCollection 2022.

Authors

Fei He¹, Fan Zhang¹, Xueqian Jiang¹, Ruicai Long¹, Zhen Wang¹, Yishi Chen², Mingna Li¹, Ting Gao³, Tianhui Yang³, Chuan Wang³, Junmei Kang¹, Lin Chen¹, Qingchuan Yang¹

Affiliations

¹ Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
² Center for Monitoring of Agricultural Ecological Environment and Quality Inspection of Agricultural Products of Tianjin, Tianjin, China.
³ Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China.

Abstract

The transition to flowering at the right time is very important for adapting to local conditions and maximizing alfalfa yield. However, the understanding of the genetic basis of the alfalfa flowering time remains limited. There are few reliable genes or markers for selection, which hinders progress in genetic research and molecular breeding of this trait in alfalfa. We sequenced 220 alfalfa cultivars and conducted a genome-wide association study (GWAS) involving 875,023 single-nucleotide polymorphisms (SNPs). The phenotypic analysis showed that the breeding status and geographical origin strongly influenced the alfalfa flowering time. Our GWAS revealed 63 loci significantly related to the flowering time. Ninety-five candidate genes were detected at these SNP loci within 40 kb (20 kb up- and downstream). Thirty-six percent of the candidate genes are involved in development and pollen tube growth, indicating that these genes are key genetic mechanisms of alfalfa growth and development. The transcriptomic analysis showed that 1,924, 2,405, and 3,779 differentially expressed genes (DEGs) were upregulated across the three growth stages, while 1,651, 2,613, and 4,730 DEGs were downregulated across the stages. Combining the results of our GWAS and transcriptome analysis, in total, 38 candidate genes (7 differentially expressed during the bud stage, 13 differentially expressed during the initial flowering stage, and 18 differentially expressed during the full flowering stage) were identified. Two SNPs located in the upstream region of the Msa0888690 gene (which is involved in isop renoids) were significantly related to flowering. The two significant SNPs within the upstream region of Msa0888690 existed as four different haplotypes in this panel. The genes identified in this study represent a series of candidate targets for further research investigating the alfalfa flowering time and could be used for alfalfa molecular breeding.

Keywords: GWAS; SNP; alfalfa; flowering time; haplotypes.