Dataset Information

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

ABSTRACT:

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. 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.

SUBMITTER: Nyine M

PROVIDER: S-EPMC6820618 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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

Nyine Moses M Uwimana Brigitte B Akech Violet V Brown Allan A Ortiz Rodomiro R Doležel Jaroslav J Lorenzen Jim J Swennen Rony R

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 20190916 12

<h4>Key message</h4>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. 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 ...[more]

PMID: 31529270

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Project description:BackgroundIn plants, RNA- based gene silencing mediated by small RNAs functions at the transcriptional or post-transcriptional level to negatively regulate target genes, repetitive sequences, viral RNAs and/or transposon elements. Post-transcriptional gene silencing (PTGS) or the RNA interference (RNAi) approach has been achieved in a wide range of plant species for inhibiting the expression of target genes by generating double-stranded RNA (dsRNA). However, to our knowledge, successful RNAi-application to knock-down endogenous genes has not been reported in the important staple food crop banana.ResultsUsing embryogenic cell suspension (ECS) transformed with ß-glucuronidase (GUS) as a model system, we assessed silencing of gusAINT using three intron-spliced hairpin RNA (ihpRNA) constructs containing gusAINT sequences of 299-nt, 26-nt and 19-nt, respectively. Their silencing potential was analysed in 2 different experimental set-ups. In the first, Agrobacterium-mediated co-transformation of banana ECS with a gusAINT containing vector and an ihpRNA construct resulted in a significantly reduced GUS enzyme activity 6-8 days after co-cultivation with either the 299-nt and 19-nt ihpRNA vectors. In the second approach, these ihpRNA constructs were transferred to stable GUS-expressing ECS and their silencing potential was evaluated in the regenerated in vitro plants. In comparison to control plants, transgenic plants transformed with the 299-nt gusAINT targeting sequence showed a 4.5 fold down-regulated gusA mRNA expression level, while GUS enzyme activity was reduced by 9 fold. Histochemical staining of plant tissues confirmed these findings. Northern blotting used to detect the expression of siRNA in the 299-nt ihpRNA vector transgenic in vitro plants revealed a negative relationship between siRNA expression and GUS enzyme activity. In contrast, no reduction in GUS activity or GUS mRNA expression occurred in the regenerated lines transformed with either of the two gusAINT oligo target sequences (26-nt and 19-nt).ConclusionsRNAi-induced silencing was achieved in banana, both at transient and stable level, resulting in significant reduction of gene expression and enzyme activity. The success of silencing was dependent on the targeted region of the target gene. The successful generation of transgenic ECS for second transformation with (an)other construct(s) can be of value for functional genomics research in banana.

Project description:The "Cavendish" and "Prata" subgroups represent respectively 47% and 24% of the world banana production. Compared to world average progressing from 10.6 to 20.6 t ha-1 between 1961 and 2016, and despite sustained domestic demand and the introduction of new cultivars, banana yield in Brazil has stagnated around 14.5 t ha-1 mainly due to nutrient and water mismanagement. "Prata" is now the dominant subgroup in N-E Brazil and is fertigated at high costs. Nutrient balances computed as isometric log-ratios (ilr) provide a comprehensive understanding of nutrient relationships in the diagnostic leaf at high yield level by combining raw concentration data. Although the most appropriate method for multivariate analysis of compositional balances may be less efficient due to non-normal data distribution and limited nutrient mobility in the plant, robustness of the nutrient balance approach could be improved using Box-Cox exponents assigned to raw foliar concentrations. Our objective was to evaluate the accuracy of nutrient balances to diagnose fertigated "Prata" orchards. The dataset comprised 609 observations on fruit yields and leaf tissue compositions collected from 2010 to 2016 in Ceará state, N-E Brazil. Raw nutrient concentration ranges were ineffective as diagnostic tool due to considerable overlapping of concentration ranges for low- and high-yielding subpopulations at cutoff yield of 40 Mg ha-1. Nutrient concentrations were combined into isometric log-ratios (ilr) and normalized by Box-Cox corrections between 0 and 1 which may also account for restricted nutrient transfer from leaf to fruit. Despite reduced ilr skewness, Box-Cox coefficients did not improve model robustness measured as the accuracy of the Cate-Nelson partition between yield and the multivariate distance across ilr values. Sensitivity was 94%, indicating that low yields are attributable primarily to nutrient imbalance. There were 148 false-positive specimens (high yield despite nutrient imbalance) likely due to suboptimal nutrition, contamination, or luxury consumption. The profitability of "Prata" orchards could be enhanced by rebalancing nutrients using ilr standards with no need for Box-Cox correction.

Dataset Information

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

Key message

Publications

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

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