Genome-wide association analyses using multilocus models on bananas (Musa spp.) reveal candidate genes related to morphology, fruit quality, and yield.

Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN: 2160-1836 (Electronic) Linking ISSN: 21601836 NLM ISO Abbreviation: G3 (Bethesda) Subsets: MEDLINE

Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Bethesda, MD : Genetics Society of America, 2011-

Musa*/genetics ; Fruit*/genetics ; Polymorphism, Single Nucleotide* ; Genome-Wide Association Study* ; Quantitative Trait Loci*; Genome, Plant ; Phenotype ; Linkage Disequilibrium ; Genes, Plant ; Quantitative Trait, Heritable

Bananas (Musa spp.) are an essential fruit worldwide and rank as the fourth most significant food crop for addressing malnutrition due to their rich nutrients and starch content. The potential of their genetic diversity remains untapped due to limited molecular breeding tools. Our study examined a phenotypically diverse group of 124 accessions from the Colombian Musaceae Collection conserved in AGROSAVIA. We assessed 12 traits categorized into morphology, fruit quality, and yield, alongside sequence data. Our sequencing efforts provided valuable insights, with an average depth of about 7× per accession, resulting in 187,133 single-nucleotide polymorphisms (SNPs) against Musa acuminata (A genome) and 220,451 against Musa balbisiana (B genome). Population structure analysis grouped samples into four and five clusters based on the reference genome. By using different association models, we identified marker-trait associations (MTAs). The mixed linear model revealed four MTAs, while the Bayesian-information and linkage-disequilibrium iteratively nested keyway and fixed and random model for circulating probability unification models identified 82 and 70 MTAs, respectively. We identified 38 and 40 candidate genes in linkage proximity to significant MTAs for the A genome and B genome, respectively. Our findings provide insights into the genetic underpinnings of morphology, fruit quality, and yield. Once validated, the SNP markers and candidate genes can potentially drive advancements in genomic-guided breeding strategies to enhance banana crop improvement.
Competing Interests: Conflicts of interest The authors declare no conflicts of interest.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

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BB/P028098/1 Biotechnology and Biology Sciences Research Council; BB/CSP1720/1 BBSRC Core Strategic Programme Grant

Keywords: Musa; skim sequencing; association mapping; germplasm

Date Created: 20240522 Date Completed: 20240807 Latest Revision: 20240809

20240809

PMC11304972

10.1093/g3journal/jkae108

38775627