A journey from SSR to SNP: The first high-density genetic maps and QTLs linked to resistance to leaf spots and Tomato spotted wilt virus in peanut

Authors: AGARWAL, GAURAV - University Of Georgia; CLEVENGER, JOSH - Mars, Inc; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; WANG, HUI - University Of Georgia; SASIDAR, YADURU - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; GANGURDE, SUNIL - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; FOUNTAIN, JAKE - University Of Georgia; CHOUDHARY, DIVYA - University Of Georgia; CHULBREATH, ALBERT - University Of Georgia; LIU, XIN - Bgi Shenzhen; HUANG, GUODONG - Bgi Shenzhen; BERTIOLI, DAVID - University Of Georgia; JACKSON, SCOTT - University Of Georgia; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Guo, Baozhu

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2017
Publication Date: 12/1/2017
Citation: Agarwal, G., Clevenger, J., Pandey, M.K., Wang, H., Sasidar, Y., Gangurde, S.S., Fountain, J.C., Choudhary, D., Chulbreath, A.K., Liu, X., Huang, G., Bertioli, D.J., Jackson, S.A., Varshney, R.K., Guo, B. 2017. A journey from SSR to SNP: The first high-density genetic maps and QTLs linked to resistance to leaf spots and Tomato spotted wilt virus in peanut [abstract]. Symposium of the Crop Genetics: Present and Future: Peanut Genetics and Genomics, Hyderabad, India, December 7-8,2017

Interpretive Summary: Host resistance to diseases, such as early leaf spot (ELS), late leaf spot (LLS) and Tomato spotted wilt virus (TSWV), is critical for increasing the yield and reducing the cost for peanut farmers. With the completion of the genome sequences of two diploid ancestors of cultivated peanut, we could genotype recombinant populations (the “T” and the “S”) using whole-genome re-sequencing (WGRS) data in order to increase the map density and accuracy of QTL identification for implementation of genomics-assisted breeding (GAB) in peanut improvement. SNPs identified using WGRS data led to the development of the densest genetic maps in peanut. Genetic maps for the “T”- and the “S” recombinant populations contains 8,869 and 14,500 SNP markers with 2,156 and 3,400 loci, respectively, covering a total map distance of 3,120 and 3,201 cM. These two maps have a marker density of 1.45 and 0.93 cM/marker locus for the “T”- and the “S”-populations, respectively. The genetic maps showed both homoeologous and translocated markers with the “T” having 739 as homeologus and 413 as translocated markers, while, the “S” showed 2422 SNPs as homeologus and 852 as translocated. For the “T”-population, there were identified a total of 35 main-effect QTLs (M-QTLs) for all three diseases with phenotypic variation explained (PVE) ranging from 6.32 to 47.63%. QTL with above 40% PVE were obtained for each of the three diseases. QTL analysis revealed that a segment of chromosome A03 substantially contributes to disease resistance. This region features major QTLs for ELS, LLS and TSWV in different capacities in terms of PVE, additive genetic effects and physical distance. KASP markers were developed for the SNPs associated with major QTLs and validated in population. Markers showed good correlation with the phenotyping data implying its potential use in genomics-assisted breeding (GAB).

Technical Abstract: Host resistance to diseases, such as early leaf spot (ELS), late leaf spot (LLS) and Tomato spotted wilt virus (TSWV), is critical for increasing the yield and reducing the cost for peanut farmers. With the completion of the genome sequences of two diploid ancestors of cultivated peanut, we could genotype recombinant populations (the “T” and the “S”) using whole-genome re-sequencing (WGRS) data in order to increase the map density and accuracy of QTL identification for implementation of genomics-assisted breeding (GAB) in peanut improvement. SNPs identified using WGRS data led to the development of the densest genetic maps in peanut. Genetic maps for the “T”- and the “S” recombinant populations contains 8,869 and 14,500 SNP markers with 2,156 and 3,400 loci, respectively, covering a total map distance of 3,120 and 3,201 cM. These two maps have a marker density of 1.45 and 0.93 cM/marker locus for the “T”- and the “S”-populations, respectively. The genetic maps showed both homoeologous and translocated markers with the “T” having 739 as homeologus and 413 as translocated markers, while, the “S” showed 2422 SNPs as homeologus and 852 as translocated. For the “T”-population, there were identified a total of 35 main-effect QTLs (M-QTLs) for all three diseases with phenotypic variation explained (PVE) ranging from 6.32 to 47.63%. QTL with above 40% PVE were obtained for each of the three diseases. QTL analysis revealed that a segment of chromosome A03 substantially contributes to disease resistance. This region features major QTLs for ELS, LLS and TSWV in different capacities in terms of PVE, additive genetic effects and physical distance. KASP markers were developed for the SNPs associated with major QTLs and validated in population. Markers showed good correlation with the phenotyping data implying its potential use in genomics-assisted breeding (GAB).