Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress

Xueming Dong,Zhipeng Liu,Hao Deng,Qiang Zhou,Wenxue Ma

doi:10.1186/s12864-021-07911-9

Abstract

BackgroundAlfalfa, the “queen of forage”, is the most extensively cultivated forage legume in the world. The development and yield of alfalfa are seriously limited by abiotic stress. MADS-box transcription factors are one of the largest gene families and play a pivotal role in plant development and abiotic stress. However, little is known regarding the MADS-box transcription factors in autotetraploid cultivated alfalfa.ResultsIn the present study, we identified 120 MsMADS-box genes in the alfalfa genome. Phylogenetic analysis indicated that 75 type-I MsMADS-box genes were classified into the Mα, Mβ, and Mγ subgroups, and 45 type-II MsMADS-box genes were classified into 11 subgroups. The promoter region of MsMADS-box genes containing several hormone and stress related elements. Chromosomal location analysis revealed that 117 MsMADS-box genes were unevenly distributed on 32 chromosomes, and the remaining three genes were located on unmapped scaffolds. A total of nine pairs of segmental duplications and four groups of tandem duplications were found. Expression analysis showed that MsMADS-box genes were differentially expressed in various tissues and under abiotic stresses. qRT-PCR analysis revealed that the expression profiles of eight selected MsMADS-box genes were distinct under various stresses.ConclusionsIn this study, MsMADS-box genes were identified in the cultivated alfalfa genome based on autotetraploid level, and further confirmed by Gene Ontology (GO) analysis, phylogenetic analysis, sequence features and expression analysis. Taken together, these findings will provide clues for further study of MsMADS-box functions and alfalfa molecular breeding.Our study is the first to systematically identify and characterize the MADS-box transcription factors in autotetraploid cultivated alfalfa (Medicago sativa L.), and eight MsMADS-box genes were significantly involved in response to various stresses.

Highlights

IntroductionThe “queen of forage”, is the most extensively cultivated forage legume in the world
Alfalfa, the “queen of forage”, is the most extensively cultivated forage legume in the world
Identification and Gene Ontology (GO) analysis of MsMADS-box genes in alfalfa A total of 120 MADS-box genes were identified in the alfalfa genome after removal of redundant sequences and were renamed from MsMADS001 to MsMADS120 according to their order of appearance in the genome annotation file

Summary

Introduction

The “queen of forage”, is the most extensively cultivated forage legume in the world. The development and yield of alfalfa are seriously limited by abiotic stress. MADS-box transcription factors are one of the largest gene families and play a pivotal role in plant development and abiotic stress. Transcription factors (TFs) regulate gene expression at the transcriptional level and are involved extensively in plant growth and development, organ morphogenesis, stress and hormone signal responses [1]. The MADSbox protein family is clustered into type-I and type-II groups, which might be derived from gene duplication events of the same ancestor [6]. According to differences in gene function and sequence homology, MIKCc-type genes are classified into 14 subgroups, which are defined as AG, SEP/AGL2, AGL6, AGL12, AGL15, AGL17, FLC, SQUA, TM3/SOC1, TM8, STMADS11, GGM13, and DEF/GLO [9]. MADS-box genes belonging to the same subfamily often show analogous expression patterns and related functions [10, 11]

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