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Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing

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Abstract

The diploid cotton species Gossypium arboreum possesses many favorable agronomic traits such as drought tolerance and disease resistance, which can be utilized in the development of improved upland cotton cultivars. The USDA National Plant Germplasm System maintains more than 1600 G. arboreum accessions. Little information is available on the genetic diversity of the collection thereby limiting the utilization of this cotton species. The genetic diversity and population structure of the G. arboreum germplasm collection were assessed by genotyping-by-sequencing of 375 accessions. Using genome-wide single nucleotide polymorphism sequence data, two major clusters were inferred with 302 accessions in Cluster 1, 64 accessions in Cluster 2, and nine accessions unassigned due to their nearly equal membership to each cluster. These two clusters were further evaluated independently resulting in the identification of two sub-clusters for the 302 Cluster 1 accessions and three sub-clusters for the 64 Cluster 2 accessions. Low to moderate genetic diversity between clusters and sub-clusters were observed indicating a narrow genetic base. Cluster 2 accessions were more genetically diverse and the majority of the accessions in this cluster were landraces. In contrast, Cluster 1 is composed of varieties or breeding lines more recently added to the collection. The majority of the accessions had kinship values ranging from 0.6 to 0.8. Eight pairs of accessions were identified as potential redundancies due to their high kinship relatedness. The genetic diversity and genotype data from this study are essential to enhance germplasm utilization to identify genetically diverse accessions for the detection of quantitative trait loci associated with important traits that would benefit upland cotton improvement.

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Acknowledgments

This research was funded by the USDA-ARS project 6066-22000-074-00D. This research was supported in part by an appointment to the Agricultural Research Service (ARS) Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the US Department of Energy (DOE) and the US Department of Agriculture (USDA). ORISE is managed by ORAU under DOE contract number DE-AC05-06OR23100. All opinions expressed in this paper are the author’s and do not necessarily reflect the policies and views of USDA, ARS, DOE, or ORAU/ORISE. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.

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  1. Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, PO Box 345, Stoneville, MS, 38776, USA

    Ruijuan Li & John E. Erpelding

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  1. Ruijuan Li
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Correspondence to John E. Erpelding.

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Supplementary material 1 (XLSX 8795 kb)

10709_2016_9921_MOESM2_ESM.tiff

Supplementary material 2 Fig. 1 Distribution of (a) locus level missing data rate, (b) minor allele frequency, and (c) heterozygosity for the initial 61,822 SNPs, preprocessed 18,571 SNPs, and discriminating 6224 SNPs. (d) Taxa level missing data rate for the 6224 discriminating SNPs (TIFF 97 kb)

10709_2016_9921_MOESM3_ESM.tiff

Supplementary material 3 Fig. 2 Plot of Delta K for (a) all 375 Gossypium arboreum accessions indicating two major clusters, (b) 302 Cluster 1 accessions showing two sub-clusters, and (c) 64 Cluster 2 accessions showing three sub-clusters (TIFF 360 kb)

10709_2016_9921_MOESM4_ESM.tiff

Supplementary material 4 Fig. 3 Population structure at different clustering level for the 6224 discriminating SNPs (TIFF 228 kb)

10709_2016_9921_MOESM5_ESM.tiff

Supplementary material 5 Fig. 4 Distribution of (a) missing data rate, (b) minor allele frequency, and (c) heterozygosity at the locus level for the 375 Gossypium arboreum accessions, 302 Cluster 1, and 64 Cluster 2 accessions (TIFF 3021 kb)

Supplementary material 6 Fig. 5 Locus level Fst distribution for the 375 accessions (TIFF 22 kb)

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Li, R., Erpelding, J.E. Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing. Genetica 144, 535–545 (2016). https://doi.org/10.1007/s10709-016-9921-2

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