Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time.

IF 7.6 Q1 GENETICS & HEREDITY 园艺研究(英文) Pub Date : 2023-09-25 eCollection Date: 2023-10-01 DOI:10.1093/hr/uhad193
Felipe Pérez de Los Cobos, Eva Coindre, Naima Dlalah, Bénédicte Quilot-Turion, Ignasi Batlle, Pere Arús, Iban Eduardo, Henri Duval
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Abstract

Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

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杏仁群体基因组学和非加性GWAS揭示了对杏仁传播史、坚果性状和开花时间的候选基因的新见解。
驯化极大地改变了作物基因组,固定了感兴趣的等位基因,并创造了不同的遗传群体。全基因组关联研究(GWAS)是检测这些感兴趣的等位基因(以及QTL)的有力工具。在本研究中,我们对243份杏仁材料的遗传结构以及加性和非加性基因型表型关联进行了探索。我们的遗传结构分析有力地支持将材料细分为五个祖先群体,所有这些群体都是由具有共同起源的材料形成的。其中一个群体完全由西班牙的材料形成,而其他群体主要由中国、意大利、法国和美国的材料形成。这些结果与考古和历史证据一致,这些证据将现代杏仁传播分为四个阶段:亚洲、地中海、加利福尼亚和南半球。我们总共发现了13个独立的QTL,分别用于坚果重量、开裂率、双仁率和开花时间。在发现的13个QTL中,只有一个具有加性效应。通过候选基因分析,我们提出Prudul26A013473是负责裂出率中发现的主要QTL的候选基因,Prudul26 A012082和Prudul26%A017782是负责双粒率中发现QTL的候选者基因,Prudel26A00954是负责开花期发现的QTL的候选基因。我们的研究提高了我们对杏仁传播史的了解,并将对杏仁育种产生重大影响。
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