García-Fernández Carmen, Campa Ana, Garzón Alvaro Soler, Miklas Phil, Ferreira Juan Jose
Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain.
Washington State Univ., Irrigated Agriculture Research and Extension Center, Prosser, Washington, 99350, USA.
BMC Plant Biol. 2021 Apr 17;21(1):184. doi: 10.1186/s12870-021-02967-x.
Common bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, condition pod morphological traits. However, not all them have been mapped or validated nor candidate genes proposed. We sought to investigate the genomic regions conditioning pod morphological and color characters through GWAS.
Single and multi-locus genome wide association analysis was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two seasons and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with 28 previously reported QTL. Twenty-one potential candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML4 affecting silique size. Eight potential candidate genes involved in pigment synthesis, were found underlying five QTL for pod color.
GWAS for pod morphological and color characters in the bean Spanish Diversity Panel revealed 62 QTL, 18 co-localized with previously reported QTL, and 16 QTL were underlain by 25 candidate genes. Overall 44 new QTL identified and 18 existing QTL contribute to a better understanding of the complex inheritance of pod size and color traits in common bean and open the opportunity for future validation works.
菜豆（Phaseolus vulgaris L.）是一种重要的豆科植物，其未成熟豆荚以及复水和烹饪后的干种子均可食用。许多基因和数量性状位点（QTL）以及它们之间的上位性相互作用决定了豆荚的形态特征。然而，并非所有这些基因和QTL都已被定位、验证或提出候选基因。我们试图通过全基因组关联研究（GWAS）来研究决定豆荚形态和颜色特征的基因组区域。
利用单基因座和多基因座全基因组关联分析，对西班牙多样性群体（SDP）的301份菜豆品系的豆荚性状进行了研究。通过测序基因分型获得32,812个单核苷酸多态性（SNP）对SDP进行基因分型。该群体在两个季节种植，并记录了17个新鲜豆荚性状的表型数据，这些性状分为四个豆荚特征：豆荚长度、豆荚横截面积、豆荚颜色和每荚种子数。总共检测到23个控制豆荚长度的QTL、6个控制横截面积的QTL、18个控制豆荚颜色的QTL、6个控制每荚种子数的QTL以及9个与两个或更多豆荚特征相关的QTL。大多数QTL位于染色体Pv01、Pv02、Pv04、Pv08、Pv09和Pv10的端粒区域。18个检测到的QTL与之前报道的28个QTL共定位。在11个控制豆荚形态特征的QTL中检测到21个涉及发育过程的潜在候选基因，其中4个与影响角果大小的拟南芥基因FIS2、SPL10、TTG2和AML4同源。在5个控制豆荚颜色的QTL中发现了8个参与色素合成的潜在候选基因。
对菜豆西班牙多样性群体的豆荚形态和颜色特征进行GWAS分析，共鉴定出62个QTL，其中18个与之前报道的QTL共定位，16个QTL由25个候选基因支撑。总体而言，新鉴定出44个QTL，18个已有的QTL有助于更好地理解菜豆豆荚大小和颜色性状的复杂遗传，并为未来的验证工作提供了机会。
