Location: Crop Genetics ResearchTitle: Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing Author
|Li, Ruijuan - Oak Ridge National Laboratory|
Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2016
Publication Date: 10/8/2016
Citation: Li, R., Erpelding, J.E. 2016. Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing. Genetica. 144:535-545. doi:10.1007/s10709-016-9921-2.
Interpretive Summary: Reniform nematode is a microscope worm that is found in the soil, infects the root system of cotton plants, and is a major pest problem in cotton production for the southeastern United States. Resistance to the nematode is lacking in upland cotton varieties. However, resistance has been found in Asiatic cotton. Transferring genes from Asiatic cotton to upland cotton can help in the development of new resistant upland cotton varieties. Nonetheless, this process is cumbersome and requires specialized breeding approaches because Asiatic cotton has half the number of chromosomes as upland cotton. With more than 1,600 Asiatic cotton varieties in the USDA, National Plant Germplasm System cotton collection, information is needed on the genetic diversity of the Asiatic cotton varieties to identify new sources of reniform nematode resistance and develop DNA markers associated with resistance to aid in the transfer of resistance to upland cotton. A genetic diversity study was conducted for 375 Asiatic cotton varieties from the germplasm collection. DNA sequencing data were used to compare the varieties and the varieties were divided into two major groups. One group included 302 varieties and many varieties tended to cluster together indicating low genetic diversity between these varieties. However, other varieties did not cluster together indicating greater genetic diversity for these varieties. Resistance to reniform nematode has been observed for 122 varieties included in the study and the data from this study will be used to select varieties with greater genetic diversity to identify varieties with different genes for reniform nematode resistance. As the genes for nematode resistance are identified, the DNA sequencing data from this study will be used to develop DNA markers associated with resistance that can be used to more rapidly transfer the resistance genes to upland cotton.
Technical 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 1,600 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 resulting in the identification of two sub-clusters for the 302 Cluster 1 accessions and three sub-clusters for the 64 Cluster 2 accessions. Approximately 54% of the accessions were in one sub-cluster indicating a narrow genetic base. In contrast, Cluster 2 accessions showed higher levels of genetic diversity. Although an association between the pattern of population structure and geographic origin was observed, not all accessions from an individual country clustered together, which is probably due to the breeding history of G. arboreum accessions and germplasm exchange. This is the first genotyping-by-sequencing study on the G. arboreum germplasm collection. Results of this study will be useful for the detection of quantitative trait loci associated with important traits from G. arboreum accessions and the introgression of these traits into upland cotton.