Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans

Author(s)

Diniz, Augusto Lima ^[1] ; Giordani, Willian ^[1] ; Costa, Zirlane Portugal ^[1] ; Margarido, Gabriel R. A. ^[1] ; Perseguini, Juliana Morini K. C. ^{[2, 3]} ; Benchimol-Reis, Luciana L. ^[2] ; Chiorato, Alisson F. ^[4] ; Garcia, Antonio Augusto F. ^[1] ; Carneiro Vieira, Maria Lucia ^[1]

Affiliation

^[1] Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, BR-13418900 Piracicaba, SP - Brazil

^[2] Inst Agron Campinas, Ctr Recursos Genet, BR-13075630 Campinas, SP - Brazil

^[3] Univ Tecnol Fed Parana, BR-85660000 Dois Vizinhos, Parana - Brazil

^[4] Inst Agron Campinas, Ctr Graos & Fibras, BR-13075630 Campinas, SP - Brazil

• Document type: Journal article
• Source: GENES; v. 10, n. 1 JAN 2019.
• Web of Science Citations: 1

Abstract

Phaseolus vulgaris is an important grain legume for human consumption. Recently, association mapping studies have been performed for the species aiming to identify loci underlying quantitative variation of traits. It is now imperative to know whether the linkage disequilibrium (LD) reflects the true association between a marker and causative loci. The aim of this study was to estimate and analyze LD on a diversity panel of common beans using ordinary r(2) and r(2) extensions which correct bias due to population structure (r(s)(2)), kinship (r(v)(2)), and both (r(vs)(2)). A total of 10,362 single nucleotide polymorphisms (SNPs) were identified by genotyping by sequencing (GBS), and polymorphisms were found to be widely distributed along the 11 chromosomes. In terms of r(2), high values of LD (over 0.8) were identified between SNPs located at opposite chromosomal ends. Estimates for r(v)(2) were lower than those for r(s)(2). Results for r(v)(2) and r(vs)(2) were similar, suggesting that kinship may also include information on population structure. Over genetic distance, LD decayed to 0.1 at a distance of 1 Mb for r(vs)(2). Inter-chromosomal LD was also evidenced. This study showed that LD estimates decay dramatically according to the population structure, and especially the degree of kinship. Importantly, the LD estimates reported herein may influence our ability to perform association mapping studies on P. vulgaris. (AU)

• FAPESP's process: 14/06647-9 - Identification of genomic regions associated with iron and zinc content in common bean seeds using associative mapping
• Grantee: Augusto Lima Diniz
• Support Opportunities: Scholarships in Brazil - Doctorate