Genome wide association analysis for biomass related traits in common vetch (Vicia sativa L.).

IF 4.1 2区生物学 Q1 PLANT SCIENCES

Frontiers in Plant Science Pub Date : 2025-09-29 eCollection Date: 2025-01-01 DOI:10.3389/fpls.2025.1647985

Hui Jin, Jumei Zhang, Yordan Dimtrov, Xue Yang, Ruonan Du, Yu-E Wu, Danna Chang, Rui Zhang, Haibin Zhao

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引用次数: 0

Abstract

Introduction: Common vetch (Vicia sativa L.) is a leguminous plant widely cultivated in Asia, Europe, and the Americas, primarily used as a forage crop and green manure.

Materials and methods: To identify loci significantly associated with biomass related traits, a genome-wide association study (GWAS) was perdormed in 172 common vetch accessions mainly from China and Europe. The single nucleotide polymorphisms (SNPs) were obtained through re-sequencing, while five biomass related traits, including the fresh weight (FW), dry weight (DW), fresh weight per plant (PFW), dry weight per plant (PDW) and plant height (PH), were evaluated across four environments.

Results: In total, 33 loci were identified, and explain 11.6-22.5% of the phenotypic variances. Notably, among them, qPDW1.2 and qPFW1.3, qPH2.1 and qFW2.1, qDW4.1 and qFW4.1, qPH5.1 and qPH5.1, qDW6.1 and qFW6.1 are overlapped or located in the same genomic region, exhibiting pleiotropic effects on two traits, and should be prioritized in further vetch breeding programs. Additionally, all the 33 loci are novel compared with previous reports. Fifteen candidate genes for biomass related traits were identified for biomass related traits, encoding ethylene-responsive transcription factors, ABC transporter family proteins, serine/threonine-protein phosphatase, cellulose synthase, and auxin-responsive proteins. Furthermore, we successfully developed and verified a kompetitive allele-specific PCR (KASP) marker (Kasp-DW1.1) for dry weight. Accessions with more favorable alleles, superior biomass related traits and agronomic traits, eg. GLF295, GLF299, GLF313, GLF321, GLF325, GLF328, GLF329, GLF330, GLF331, GLF335, HZMC1382 and HZMC1487 are recommended as parental lines for further common vetch breeding.

Discussion: This study enhances our understanding of the genetic architecture of biomass related traits and provides available novel loci, molecular tools and outstanding varieties for improving common vetch biomass in future breeding.

Abstract Image

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豇豆生物量相关性状的全基因组关联分析。

简介：野豌豆（Vicia sativa L.）是一种豆科植物，广泛种植于亚洲、欧洲和美洲，主要用作饲料作物和绿肥。材料与方法：对来自中国和欧洲的172份常见野豌豆材料进行了全基因组关联研究（GWAS），以确定与生物量相关性状显著相关的位点。通过重测序获得了单核苷酸多态性（snp），并对4种环境下的5个生物量相关性状进行了评价，包括鲜重（FW）、干重（DW）、单株鲜重（PFW）、单株干重（PDW）和株高（PH）。结果：共鉴定出33个基因座，解释了11.6% ~ 22.5%的表型变异。值得注意的是，其中qPDW1.2和qPFW1.3、qPH2.1和qFW2.1、qDW4.1和qFW4.1、qPH5.1和qPH5.1、qDW6.1和qFW6.1重叠或位于同一基因组区域，对这两个性状具有多效性，应在进一步的育种规划中优先考虑。此外，与以往报道相比，所有33个基因座都是新的。生物量相关性状的15个候选基因分别编码乙烯应答转录因子、ABC转运蛋白家族蛋白、丝氨酸/苏氨酸蛋白磷酸酶、纤维素合成酶和生长素应答蛋白。此外，我们成功开发并验证了干重竞争性等位基因特异性PCR （KASP）标记（KASP - dw1.1）。具有较好等位基因、生物量相关性状和农艺性状较优的材料。GLF295、GLF299、GLF313、GLF321、GLF325、GLF328、GLF329、GLF330、GLF331、GLF335、HZMC1382和HZMC1487是推荐的亲本品种。讨论：本研究增强了我们对生物量相关性状遗传结构的认识，为今后提高普通野豌豆生物量的育种提供了新的位点、分子工具和优秀品种。

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来源期刊

Frontiers in Plant Science PLANT SCIENCES-

CiteScore

7.30

自引率

14.30%

发文量

4844

审稿时长

14 weeks

期刊介绍： In an ever changing world, plant science is of the utmost importance for securing the future well-being of humankind. Plants provide oxygen, food, feed, fibers, and building materials. In addition, they are a diverse source of industrial and pharmaceutical chemicals. Plants are centrally important to the health of ecosystems, and their understanding is critical for learning how to manage and maintain a sustainable biosphere. Plant science is extremely interdisciplinary, reaching from agricultural science to paleobotany, and molecular physiology to ecology. It uses the latest developments in computer science, optics, molecular biology and genomics to address challenges in model systems, agricultural crops, and ecosystems. Plant science research inquires into the form, function, development, diversity, reproduction, evolution and uses of both higher and lower plants and their interactions with other organisms throughout the biosphere. Frontiers in Plant Science welcomes outstanding contributions in any field of plant science from basic to applied research, from organismal to molecular studies, from single plant analysis to studies of populations and whole ecosystems, and from molecular to biophysical to computational approaches. Frontiers in Plant Science publishes articles on the most outstanding discoveries across a wide research spectrum of Plant Science. The mission of Frontiers in Plant Science is to bring all relevant Plant Science areas together on a single platform.