Genomic markers linked to Meloidogyne chitwoodi resistance introgressed from Solanum bulbocastanum to cultivated potato and their utility in marker-assisted selection

Sapinder Bali; Charles Brown; Hassan Majtahedi; Solomon Yilma; Russell E Ingham; Launa Cimrhakl; Rich Quick; Vidyasagar Sathuvalli

doi:10.1007/s11032-022-01285-w

Genomic markers linked to Meloidogyne chitwoodi resistance introgressed from Solanum bulbocastanum to cultivated potato and their utility in marker-assisted selection

Mol Breed. 2022 Mar 2;42(3):12. doi: 10.1007/s11032-022-01285-w. eCollection 2022 Mar.

Authors

Sapinder Bali^{1

2}, Charles Brown³, Hassan Majtahedi³, Solomon Yilma⁴, Russell E Ingham⁵, Launa Cimrhakl³, Rich Quick³, Vidyasagar Sathuvalli¹

Affiliations

¹ Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston-97838, OR USA.
² Department of Plant Pathology, Washington State University, Pullman-99164, WA USA.
³ Temperate Tree Fruit and Vegetable Research Unit, USDA-Agricultural Research Service, Prosser-99350, WA USA.
⁴ Department of Crop and Soil Sciences, Oregon State University, Corvallis-97331, OR USA.
⁵ Department of Botany and Plant Pathology, Oregon State University, Corvallis-97333, OR USA.

Abstract

Meloidogyne chitwoodi is a major threat to potato production in the Pacific Northwest region of the United States. Infected tubers are rendered unmarketable; hence, growers' profitability is adversely affected. Breeding for nematode resistance is a long-term process and phenotyping the segregating populations for nematode resistance is the most time-consuming and laborious part of the process. Using DNA-based markers closely linked to the nematode resistance trait for marker-assisted selection (MAS) could enhance breeding efficiency and accuracy. In the present study, a pool of phenotyped progenies segregating for nematode resistance and susceptibility were fingerprinted using a 21 K single-nucleotide polymorphism (SNP) array. Eight candidate SNPs located on potato Chromosome 11, segregating with the nematode resistance trait, were identified and used as landmarks for discovery of other marker types such as simple sequence repeat (SSR) and insertion-deletion (INDEL) markers. Subsequently, a total of eight SNPs, 30 SSRs, and four INDELS located on scaffold 11 of Solanum bulbocastanum were used to design primers; markers were validated in a panel of resistant and susceptible clones. Two SNPs (SB_MC1Chr11-PotVar0066518 and SB_MC1Chr11-PotVar0064140), five SSRs (SB_MC1Chr11-SSR04, SB_MC1Chr11-SSR08, SB_MC1Chr11-SSR10, SB_MC1Chr11-SSR13, and SB_MC1Chr11-SSR20), and one INDEL (SB_MC1Chr11-INDEL4) markers showed polymorphism between the resistant and susceptible clones in the test panel and in other segregating progenies. These markers are robust, highly reproducible, and easy to use for MAS of nematode-resistant potato clones to enhance the breeding program.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-022-01285-w.

Keywords: Columbia root-knot nematode; High-throughput SNPs; INDEL markers; Nematode resistance; Resistance breeding; SSR markers.