Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 May 4;11(5):e0154448.
doi: 10.1371/journal.pone.0154448. eCollection 2016.

A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop

Julie Sardos  1 , Mathieu Rouard  1 , Yann Hueber  1 , Alberto Cenci  1 , Katie E Hyma  2 , Ines van den Houwe  3 , Eva Hribova  4 , Brigitte Courtois  5 , Nicolas Roux  1
Affiliations

A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop

Julie Sardos et al. PLoS One. .

Abstract

Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1
Fruits of a. M. acuminata banksii ITC0766 ‘Paliama’, wild and seeded, b. diploid AA ITC1121 ‘Pisang Lilin’ (synonym of ITC0395 ‘Lidi’) cultivated and unseeded and c. triploid ABB ITC0361 ‘Blue Java’ cultivated and occasionally setting seeds. Credits: B. Irish (USDA-ARS) for the Taxonomic Reference Collection exercise.
Fig 2
Fig 2. Genetic structure of the panel.
STRUCTURE outputs: a. LnP(D) and its variance across 8 runs for each values of K, from 1 to 10, based on the genotypic data available for 498 DArT markers and b. Representation of the admixture pattern of the panel for K = 4 as calculated on the genotypic data obtained with the 5544 SNPs of the study, each bar corresponds to a genotype and colours correspond to the detected genetic clusters. c. NJ tree conducted on a Simple Matching dissimilarity matrix. Coloured branches correspond to unadmixed accessions (Q > 0.8) and black branches to admixed accessions (Q< 0.8) at K = 4.
Fig 3
Fig 3. Scatter plots of LD (r²) for all 1,417,890 marker pairs as a function of physical distance (bp) for the full panel composed of 104 diploid Musa accessions with a pure M. acuminata genetic background as calculated by HAPLOVIEW.
LD decay curve fitted by the GAM function is represented by the blue line.
Fig 4
Fig 4. GWAS for the seedless phenotype (MAF > 10%).
Quantile-Quantile plots and corresponding Manhattan plots obtained on the Panel using simple GLM (a-b) and uncompressed MLM K + Q (k = 4) (c-d) and the Papuan Subset using simple GLM (e-h) and uncompressed MLM K (g-h). Colored dashed lines correspond to Bonferroni corrected thresholds of p = 0.05 (blue) and p = 0.01 (red).
Fig 5
Fig 5. Local association plot for the approximate 184 kb candidate region detected on chromosome 7 and LD maps for the entire chromosome and the corresponding region.
Dashed lines indicate the most significant associations.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Available: http://faostat3.fao.org/home/E. In: FAOstat.
    1. De Langhe E, Langhe ED, Vrydaghs L, Maret P de, Perrier X, Denham T. Why Bananas Matter: An introduction to the history of banana domestication. Ethnobot Res Appl. 2009;7: 165–177. 10.17348/era.7.0.165-177 - DOI
    1. Perrier X, De Langhe E, Donohue M, Lentfer C, Vrydaghs L, Bakry F, et al. Multidisciplinary perspectives on banana (Musa spp.) domestication. Proc Natl Acad Sci. 2011; 10.1073/pnas.1102001108 - DOI - PMC - PubMed
    1. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010;42: 961–967. 10.1038/ng.695 - DOI - PubMed
    1. Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, et al. Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol. 2012;12: 16 10.1186/1471-2229-12-16 - DOI - PMC - PubMed

Publication types

Grants and funding

This study was funded by RTB, the CGIAR Research Program on Roots, Tubers and bananas (http://www.rtb.cgiar.org/) through the cross-cutting project entitled "Enhancing global RTB productivity through more targeted use of global RTB genetic Diversity" led by Dr. Augusto Becerra-Lopez-Lavalle (CIAT) and DR. Nicolas Roux (Bioversity International). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.