Genome-wide association study revealed some new candidate genes associated with flowering and maturity time of soybean in Central and West Siberian regions of Russia.

IF 4.1 2区 生物学 Q1 PLANT SCIENCES
Frontiers in Plant Science Pub Date : 2024-10-11 eCollection Date: 2024-01-01 DOI:10.3389/fpls.2024.1463121
Roman Perfil Ev, Andrey Shcherban, Dmitriy Potapov, Konstantin Maksimenko, Sergey Kiryukhin, Sergey Gurinovich, Veronika Panarina, Revmira Polyudina, Elena Salina
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Abstract

The duration of flowering and maturity is an important agricultural trait determining the suitability of a variety for cultivation in the target region. In the present study, we used genome-wide association analysis (GWAS) to search for loci associated with soybean flowering and maturity in the Central and West Siberian regions of Russia. A field experiment was conducted in 2021/2022 at two locations (Orel and Novosibirsk). A germplasm collection of 180 accessions was genotyped using SoySNP50K Illumina Infinium Bead-Chip. From the initial collection, we selected 129 unrelated accessions and conducted GWAS on this dataset using two multi-locus models: FarmCPU and BLINK. As a result, we identified 13 loci previously reported to be associated with duration of soybean development, and 17 new loci. 33 candidate genes were detected in these loci using analysis of co-expression, gene ontology, and literature data, with the best candidates being Glyma.03G177500, Glyma.13G177400, and Glyma.06G213100. These candidate genes code the Arabidopis orthologs TOE1 (TARGET OF EAT 1), SPL3 (SQUAMOSA PROMOTER BINDING PROTEIN LIKE 3), the DELLA protein, respectively. In these three genes, we found haplotypes which may be associated with the length of soybean flowering and maturity, providing soybean adaptation to a northern latitudes.

全基因组关联研究发现了一些与俄罗斯中西伯利亚地区大豆开花和成熟时间相关的新候选基因。
开花期和成熟期是决定一个品种是否适合在目标地区种植的重要农业性状。在本研究中,我们利用全基因组关联分析(GWAS)寻找与俄罗斯中西伯利亚地区大豆开花期和成熟期相关的基因位点。2021/2022 年,我们在两个地点(奥廖尔和新西伯利亚)进行了田间试验。使用 SoySNP50K Illumina Infinium Bead-Chip 对收集的 180 份种质进行了基因分型。我们从最初收集的数据中选择了 129 个不相关的品种,并使用两个多焦点模型对该数据集进行了 GWAS 分析:FarmCPU 和 BLINK。结果,我们发现了 13 个以前报道过的与大豆发育期相关的基因位点,以及 17 个新的基因位点。通过对共表达、基因本体和文献数据的分析,在这些位点上发现了 33 个候选基因,其中最佳候选基因为 Glyma.03G177500、Glyma.13G177400 和 Glyma.06G213100。这些候选基因分别编码阿拉比多糖直向同源物 TOE1(TARGET OF EAT 1)、SPL3(SQUAMOSA PROMOTER BINDING PROTEIN LIKE 3)和 DELLA 蛋白。在这三个基因中,我们发现了可能与大豆开花期和成熟期的长短有关的单倍型,为大豆适应北方纬度提供了依据。
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来源期刊
Frontiers in Plant Science
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.
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