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

Autor: Diniz AL; Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil. augustold@usp.br., Giordani W; Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil. giordani.willian@usp.br., Costa ZP; Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil. zirlane26@gmail.com., Margarido GRA; Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil. gramarga@usp.br., Perseguini JMKC; Universidade Tecnológica Federal do Paraná, Dois Vizinhos, Paraná 85660-000, Brazil. julianamorini@hotmail.com.; Centro de Recursos Genéticos, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil. julianamorini@hotmail.com., Benchimol-Reis LL; Centro de Recursos Genéticos, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil. julianamorini@hotmail.com., Chiorato AF; Centro de Grãos e Fibras, Instituto Agronômico de Campinas, Campinas, São Paulo 13075-630, Brazil. afchiorato@iac.sp.gov.br., Garcia AAF; Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil. augusto.garcia@usp.br., Vieira MLC; Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil. mlcvieir@usp.br.
Jazyk: angličtina
Zdroj: Genes [Genes (Basel)] 2018 Dec 21; Vol. 10 (1). Date of Electronic Publication: 2018 Dec 21.
DOI: 10.3390/genes10010005
Abstrakt: 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 r² 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 r2, 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 .
Competing Interests: The authors declare no conflict of interest.
Databáze: MEDLINE
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