A digital catalog of high‐density markers for banana germplasm collections

Rouard, Mathieu; Sardos, Julie; Sempéré, Guilhem; Breton, Catherine; Guignon, Valentin; houwe, Ines Van den; Carpentier, Sébastien; Roux, Nicolás

doi:10.1002/ppp3.10187

Cited by 9 publications

(5 citation statements)

References 40 publications

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“…The underlying genetics in banana are still challenging due to their long growth cycles, the logistics of performing high-throughput screenings, and the high variability in the phenotypic data, as reflected in this study. Despite these difficulties, the availability of the Musa draft genome assemblies and lower whole genome genotyping/sequencing costs have facilitated studies in SNP discovery, genome evolution, and population genetics in banana [65][66][67][68][69]. With Foc-TR4 edging closer to the major banana growing regions of Latin America [70], it becomes ever more important to dissect host resistance against Foc-TR4 and, in doing so, to identify potential resistance genes that underpin the Foc-TR4 resistance per se.…”

Section: Discussionmentioning

confidence: 99%

Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Chen¹,

Sun²,

Viljoen³

et al. 2023

Preprint

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Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. malaccensis segregating populations segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on Chromosome 3 of ‘DH-Pahang’ reference assembly v4. Within this region, there is a cluster of pattern recognition receptors, namely leucine rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell wall associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant but not in susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent ‘Ma850’ and a susceptible line ‘Ma848’, to show that the STR4 resistance co-segregated with marker ‘28820’ at this locus. Finally, an informative SNP marker 29730 allowed the locus specific resistance to be assessed in a collection of diploid and polyploid banana plants. Out of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4 resistant, such as ‘Pahang’, ‘SH-3362’, ‘SH-3217’, ‘Ma-ITC0250’, and ‘DH-Pahang/CIRAD 930’. Additional screening in the International Institute for Tropical Agriculture’s collection suggests that the dominant allele is common among in the elite ‘Matooke’ NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine-mapping and candidate gene identification will allow characterization of molecular mechanisms underlying TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.

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Section: Discussionmentioning

confidence: 99%

Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Chen¹,

Sun²,

Viljoen³

et al. 2023

Preprint

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“…Common cultivars were still absent in our panel (Ambon, Rio, Orotava, etc.). Since accessions held in genebanks other than the ITC have not been genotyped ( Rouard et al 2021 ), we verified or corrected the passport information based on the genetic analysis in Supplementary Data Table S1 .…”

Section: Discussionmentioning

confidence: 99%

Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages

Higgins,

Osorio-Guarín,

Olave-Achury

et al. 2023

Annals of Botany

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Background Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation. Methods We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination. Results In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties. Conclusions We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.

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“…This population and its wild counterpart are represented in our samples by 31 and 24 accessions respectively. A set of 238,357 SNPs was retrieved from GIGWA (Sempeŕéet al, 2019;Rouard et al, 2022) allowing a maximum of 50% of missing data for each of the two populations. Using VCFtools, we first assessed observed heterozygosity (Ho) and inbreeding coefficient (F) for each of these accessions.…”

Section: Population Differentiation Between Wild and Cultivated Papua...mentioning

confidence: 99%

Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas

Sardos¹,

Breton²,

Perrier³

et al. 2022

Front. Plant Sci.

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Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.

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A digital catalog of high‐density markers for banana germplasm collections

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 9 publications

References 40 publications

Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages

Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas

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