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Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group)

Bunch weight increase is one of the major objectives of banana improvement programs, but little is known about the loci controlling bunch weight and its component traits. Here we report for the first time some genomic loci associated with bunch weight and its component traits in banana as revealed through a genome-wide association study. A banana-breeding population of 307 genotypes varying in ploidy was phenotyped in three locations under different environmental conditions, and data were collected on bunch weight, number of hands and fruits

Moses Nyine, Brigitte Uwimana, Violet Akech, Allan Brown, Rodomiro Ortiz,  Jaroslav Doležel, Jim Lorenzen, Rony Swennen

Theoretical and Applied Genetics; December 2019, Volume 132, Issue 12, pp 3295–3308

Key message

The major quantitative trait loci associated with bunch weight and its component traits in the East African highland banana-breeding population are located on chromosome 3.

Abstract

Bunch weight increase is one of the major objectives of banana improvement programs, but little is known about the loci controlling bunch weight and its component traits. Here we report for the first time some genomic loci associated with bunch weight and its component traits in banana as revealed through a genome-wide association study. A banana-breeding population of 307 genotypes varying in ploidy was phenotyped in three locations under different environmental conditions, and data were collected on bunch weight, number of hands and fruits; fruit length and circumference; and diameter of both fruit and pulp for three crop cycles. The population was genotyped with genotyping by sequencing and 27,178 single nucleotide polymorphisms (SNPs) were generated. The association between SNPs and the best linear unbiased predictors of traits was performed with TASSEL v5 using a mixed linear model accounting for population structure and kinship. Using Bonferroni correction, false discovery rate, and long-range linkage disequilibrium (LD), 25 genomic loci were identified with significant SNPs and most were localized on chromosome 3. Most SNPs were located in genes encoding uncharacterized and hypothetical proteins, but some mapped to transcription factors and genes involved in cell cycle regulation. Inter-chromosomal LD of SNPs was present in the population, but none of the SNPs were significantly associated with the traits. The clustering of significant SNPs on chromosome 3 supported our hypothesis that fruit filling in this population was under control of a few quantitative trait loci with major effects.

 

See https://link.springer.com/article/10.1007/s00122-019-03425-x

Figure 3: Single nucleotide polymorphisms (SNPs) associated with fruit circumference. a Quartile–quartile (Q–Q) plot showing deviation from null hypothesis of no significant association, b Manhattan plot showing location of significant SNPs, the red line indicates the Bonferroni correction threshold at a P value of 1.84e−6 (color figure online)

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