Ankush Purushottam Wankhade, Vivek Pandurang Chimote, Kannalli Paramashivaiah Viswanatha, Shasidhar Yadaru, Dnyaneshwar Bandu Deshmukh, Swathi Gattu, Hari Kishan Sudini, Milind Panjabrao Deshmukh, Vivek Shivaji Shinde, Anil Kumar Vemula & Janila Pasupuleti

Theoretical and Applied Genetics March 2023; vol. 136, Article number: 43 (2023)

Published: 10 March 2023

Key message

The identified 30 functional nucleotide polymorphisms or genic SNP markers would offer essential information for marker-assisted breeding in groundnut.

Abstract

A genome-wide association study (GWAS) on component traits of LLS resistance in an eight-way multiparent advance generation intercross (MAGIC) population of groundnut in the field and in a light chamber (controlled conditions) was performed via an Affymetrix 48 K single-nucleotide polymorphism (SNP) ‘Axiom Arachis’ array. Multiparental populations with high-density genotyping enable the detection of novel alleles. In total, five quantitative trait loci (QTLs) with marker − log10(p value) scores ranging from 4.25 to 13.77 for the incubation period (IP) and six QTLs with marker − log10(p value) scores ranging from 4.33 to 10.79 for the latent period (LP) were identified across the A- and B-subgenomes. A total of 62 markers‒trait associations (MTAs) were identified across the A- and B-subgenomes. Markers for LLS scores and the area under the disease progression curve (AUDPC) recorded for plants in the light chamber and under field conditions presented − log10 (p value) scores ranging from 4.22 to 27.30. The highest number of MTAs (six) was identified on chromosomes A05, B07 and B09. Out of a total of 73 MTAs, 37 and 36 MTAs were detected in subgenomes A and B, respectively. Taken together, these results suggest that both subgenomes have equal potential genomic regions contributing to LLS resistance. A total of 30 functional nucleotide polymorphisms or genic SNP markers were detected, among which eight genes were found to encode leucine-rich repeat (LRR) receptor-like protein kinases and putative disease resistance proteins. These important SNPs can be used in breeding programmes for the development of cultivars with improved disease resistance.

See https://link.springer.com/article/10.1007/s00122-023-04256-7