Genomic analysis reveals the interplay between ABA-GA in determining fresh seed dormancy in groundnut

IF 5.7 2区生物学 Q1 PLANT SCIENCES

Plant Physiology and Biochemistry Pub Date : 2025-09-18 DOI:10.1016/j.plaphy.2025.110539

D. Khaja Mohinuddin , Sunil S. Gangurde , Hasan Khan , Deekshitha Bomireddy , Vinay Sharma , Priya Shah , U. Nikhil Sagar , Namita Dube , Ramachandran Senthil , B.V. Tembhurne , V. Hanumanth Nayak , Ovais Hamid Peerzada , A. Amaregouda , Kisan Babu , Kuldeep Singh , Pasupuleti Janila , Baozhu Guo , Boshou Liao , Rajeev K. Varshney , Manish K. Pandey

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引用次数: 0

Abstract

Groundnut is an important oilseed crop; however, its productivity and seed quality are frequently reduced due to lack of fresh seed dormancy (FSD). To address this challenge, a mini-core collection of 184 accessions was phenotyped to identify potential donors in each agronomic type. In addition, whole genome re-sequencing and multi-season phenotypic evaluations were analyzed to identify stable marker-trait associations (MTAs) linked to FSD. Phenotypic analysis revealed substantial variability in dormancy durations, with days to 50 % germination (DFG) ranging from 1 to 30 days. Multi-locus genome-wide association study (ML-GWAS) identified 27 MTAs in individual seasons and 12 MTAs in pooled seasons data, respectively. Key candidate genes identified included Cytochrome P450 superfamily proteins, protein kinase superfamily proteins, and MYB transcription factors involved in the Abscisic acid (ABA) pathway, as well as F-box interaction domain proteins, ATP-binding ABC transporters, associated with the Gibberellic acid (GA) pathway. SNP-based KASP (Kompetitive Allele-Specific Polymerase chain reaction) markers were developed for 12 SNPs, of which four markers (snpAH00577, snpAH00580, snpAH00586 and snpAH00588) were found useful for the selection of FSD. The combination of favourable allele from four genes namely Ahfsd1 (Arahy.8B3CAL), Ahfsd2 (Arahy.NRZN5K), Ahfsd3 (Arahy.JJ8FJQ), and Ahfsd4 (Arahy.PI0JM6) provides stable 24–30 days of dormancy. Incorporating favourable dormant alleles into breeding programs could enable the development of high-yielding cultivars with a dormancy period of more than two weeks.

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基因组分析揭示了ABA-GA在决定花生新鲜种子休眠中的相互作用。

花生是重要的油料作物；然而，由于缺乏新鲜种子休眠（FSD），其产量和种子质量经常下降。为了应对这一挑战，对184份材料进行了表型分析，以确定每种农艺类型的潜在供体。此外，研究人员还分析了全基因组重测序和多季节表型评估，以确定与FSD相关的稳定标记-性状关联（mta）。表型分析显示休眠时间有很大的差异，从1天到50%萌发（DFG）从1天到30天不等。多位点全基因组关联研究（ML-GWAS）在单个季节数据中鉴定出27个mta，在汇总季节数据中鉴定出12个mta。鉴定的关键候选基因包括细胞色素P450超家族蛋白、蛋白激酶超家族蛋白、参与脱落酸（ABA）途径的MYB转录因子，以及与赤霉素（GA）途径相关的F-box相互作用结构域蛋白、atp结合ABC转运蛋白。利用KASP （competitive Allele-Specific Polymerase chain reaction，竞争性等位基因特异性聚合酶链反应）标记对12个snp进行筛选，发现4个标记（snpAH00577、snpAH00580、snpAH00586和snpAH00588）对FSD的选择有帮助。来自Ahfsd1 （Arahy. 8b3cal）、Ahfsd2 （Arahy. 8b3cal）四个基因的有利等位基因组合。NRZN5K), Ahfsd3 (Arahy。JJ8FJQ)和Ahfsd4 （Arahy.PI0JM6）提供了24-30天的稳定休眠。将有利的休眠等位基因纳入育种计划，可以培育出休眠期在两周以上的高产品种。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Plant Physiology and Biochemistry 生物-植物科学

CiteScore

11.10

自引率

3.10%

发文量

410

审稿时长

33 days

期刊介绍： Plant Physiology and Biochemistry publishes original theoretical, experimental and technical contributions in the various fields of plant physiology (biochemistry, physiology, structure, genetics, plant-microbe interactions, etc.) at diverse levels of integration (molecular, subcellular, cellular, organ, whole plant, environmental). Opinions expressed in the journal are the sole responsibility of the authors and publication does not imply the editors'' agreement. Manuscripts describing molecular-genetic and/or gene expression data that are not integrated with biochemical analysis and/or actual measurements of plant physiological processes are not suitable for PPB. Also "Omics" studies (transcriptomics, proteomics, metabolomics, etc.) reporting descriptive analysis without an element of functional validation assays, will not be considered. Similarly, applied agronomic or phytochemical studies that generate no new, fundamental insights in plant physiological and/or biochemical processes are not suitable for publication in PPB. Plant Physiology and Biochemistry publishes several types of articles: Reviews, Papers and Short Papers. Articles for Reviews are either invited by the editor or proposed by the authors for the editor''s prior agreement. Reviews should not exceed 40 typewritten pages and Short Papers no more than approximately 8 typewritten pages. The fundamental character of Plant Physiology and Biochemistry remains that of a journal for original results.