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ARS Home » Southeast Area » Tifton, Georgia » Crop Protection and Management Research » Research » Publications at this Location » Publication #347803
Title: The SNP-based high-density linkage maps and fine mapping of QTLs controlling disease resistance using whole-genome re-sequencing in peanut

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

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/15/2017
Publication Date: 1/13/2018
Citation: Guo, B., Agarwal, G., Clevenger, J., Pandey, M.K., Wang, H., Sisidar, Y., Gangurde, S.S., Fountain, J.C., Choudhary, D., Culbreath, A.K., Liu, X., Bertioli, D.J., Jackson, S.A., Varshney, R.K. 2018. The SNP-based high-density linkage maps and fine mapping of QTLs controlling disease resistance using whole-genome re-sequencing in peanut[abstract]. Annual International Plant & Animal Genome Conference, San Diego, CA.

Interpretive Summary: High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early and late leaf spots (ELS, LLS), Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use whole-genome re-sequencing (WGRS) technology to genotype recombinant inbred line (RIL) populations and develop high-density genetic maps for peanut. We constructed the first sequence-based high density maps with a total of 8,869 and 14,500 SNPs assigned to 20 linkage groups, representing the 20 chromosomes, for the “T”- and the “S” populations, respectively. The total length of the linkage maps were 3,120 and 3,201 cM with an average distance of 1.45 and 0.93 cM among 2,156 and 3,400 loci for the “T” and the “S”, 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 markers. For the “T”-population, there were 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 detected for each of the three diseases. QTL analysis revealed that a segment of chromosome A03 features major QTLs for ELS, LLS and TSWV. KASP markers were developed and validated for the SNPs associated with major QTLs, which could be used in genomics-assisted breeding (GAB).

Technical Abstract: High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early and late leaf spots (ELS, LLS), Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use whole-genome re-sequencing (WGRS) technology to genotype recombinant inbred line (RIL) populations and develop high-density genetic maps for peanut. We constructed the first sequence-based high density maps with a total of 8,869 and 14,500 SNPs assigned to 20 linkage groups, representing the 20 chromosomes, for the “T”- and the “S” populations, respectively. The total length of the linkage maps were 3,120 and 3,201 cM with an average distance of 1.45 and 0.93 cM among 2,156 and 3,400 loci for the “T” and the “S”, 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 markers. For the “T”-population, there were 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 detected for each of the three diseases. QTL analysis revealed that a segment of chromosome A03 features major QTLs for ELS, LLS and TSWV. KASP markers were developed and validated for the SNPs associated with major QTLs, which could be used in genomics-assisted breeding (GAB).