Silva Adriel Carlos da, Gregorio da Silva Danielle C, Ferreira Everton Geraldo Capote, Abdelnoor Ricardo V, Borém Aluízio, Arias Carlos Arrabal, Oliveira Marcelo F, Oliveira Marcio Elias F de, Marcelino-Guimarães Francismar Corrêa
Centro de Ciências Biológicas, Programa de Pós-Graduação em Genética Melhoramento, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
Empresa Brasileira de Pesquisa e Agropecuária-Embrapa Soja, Laboratório de Biotecnologia Vegetal e Bioinformática, Londrina, Paraná, Brazil.
PLoS One. 2025 Jan 30;20(1):e0313151. doi: 10.1371/journal.pone.0313151. eCollection 2025.
Soybean [Glycine max (L.) Merrill] is one of the most widely grown legumes in the world, with Brazil being its largest producer and exporter. Breeding programs in Brazil have resulted from multiple cycles of selection and recombination starting from a small number of USA cultivar ancestors in the 1950s and 1960s years. This process has led to the successful adaptation of this crop to tropical conditions, a phenomenon known as tropicalization. Many studies describe a narrow genetic background in Brazilian soybean cultivars. Various factors can affect the genetic diversity in species, especially in cultivated crops, such as the reproduction type, artificial selection, and the number and sources of variability in the breeding programs. In turns, the genetic diversity can affect the linkage disequilibrium blocks (LD) patterns and, consequently, molecular breeding strategies for selection of target loci for agronomic traits. We used high-throughput genotyping with SoySNP50K Illumina SNP markers to assess a collection of 370 Brazilian soybean accessions covering more than 60 years of soybean breeding in Brazil. Our goal was to investigate population structure and genetic diversity in the Brazilian germplasm, detect patterns of LD blocks, and identify regions presenting signals of selective swaps linked with quantitative trait loci (QTLs) of agronomic interest. Population structure analysis revealed two major groups among all genotypes, primarily differentiated by the year of release, separating old and new cultivars (before and after 2000´s years), and by growth habit (stem termination type-SST). The group I comprises about 75% of the panel and includes cultivars release before 2000`s years, including the oldest cultivars released in Brazil, most of which exhibit a determinate growth habit and maturity groups VI and VII. Group II includes only 83 materials, but shows higher levels of diversity than group I, representing most recent introductions in Brazilian germplasm. Further analysis of substructure within Group I, identified seven subgroups with no clear trend for segregation based on maturity group, STT or year of release. Instead, these subgroups were based on the contribution of key donors of disease resistance and adaptability, as soybean cultivation expanded from the South to Central region of Brazil. This finding is consistent with the history of soybean expansion in Brazil. We identified 123 genomic regions under selection among the groups of Brazilian cultivars associated with 440 quantitative trait loci (QTLs), revealing regions fixed across the breeding process associated with yield, disease resistance, water efficiency use, and others.
大豆[Glycine max (L.) Merrill]是世界上种植最广泛的豆科植物之一，巴西是其最大的生产国和出口国。巴西的育种计划源于20世纪50年代和60年代从少数美国栽培品种祖先开始的多轮选择和重组。这一过程导致了这种作物成功适应热带条件，这一现象被称为热带化。许多研究描述了巴西大豆品种的遗传背景狭窄。各种因素会影响物种的遗传多样性，尤其是栽培作物，如繁殖类型、人工选择以及育种计划中变异的数量和来源。反过来，遗传多样性会影响连锁不平衡块（LD）模式，从而影响用于选择农艺性状目标位点的分子育种策略。我们使用SoySNP50K Illumina SNP标记进行高通量基因分型，以评估370份巴西大豆种质资源，这些资源涵盖了巴西60多年的大豆育种历程。我们的目标是研究巴西种质资源的群体结构和遗传多样性，检测LD块模式，并识别与农艺性状数量性状位点（QTL）相关的呈现选择性交换信号的区域。群体结构分析揭示了所有基因型中的两个主要群体，主要根据发布年份区分，将旧品种和新品种（2000年之前和之后）以及生长习性（茎端终止类型-SST）区分开来。第一组占样本的约75%，包括2000年之前发布的品种，包括巴西发布的最古老品种，其中大多数表现出有限生长习性以及VI和VII成熟组。第二组仅包括83份材料，但显示出比第一组更高的多样性水平，代表了巴西种质资源中最新引入的品种。对第一组内亚结构的进一步分析确定了七个亚组，基于成熟组、SST或发布年份没有明显的分离趋势。相反，这些亚组是基于抗病性和适应性关键供体的贡献，因为大豆种植从巴西南部扩展到中部地区。这一发现与巴西大豆扩张的历史一致。我们在巴西品种组中确定了123个受选择的基因组区域，与440个数量性状位点（QTL）相关，揭示了在育种过程中固定的与产量、抗病性、水分利用效率等相关的区域。
