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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #422025
Research Project: Pecan Breeding and Management of the National Collection of Carya Genetic Resources

Location: Crop Germplasm Research

Title: A GWAS analysis of nut quality traits important to pecan (Carya illinoinensis) breeding

Author
item Chatwin, Warren
item Molik, David
item Wang, Xinwang
item Hilton, Angelyn
item Kubenka, Keith
item PROVIN, ELLEN - Texas A&M University
item Udall, Joshua
item RANDALL, JENNIFER - New Mexico State University
item MAMIDI, SUJAN - Hudsonalpha Institute For Biotechnology
item LOVELL, JOHN - Hudsonalpha Institute For Biotechnology

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/12/2024
Publication Date: 1/17/2024
Citation: Chatwin, W.B., Molik, D.C., Wang, X., Hilton, A.E., Kubenka, K.A., Provin, E., Udall, J.A., Randall, J., Mamidi, S., Lovell, J. 2024. A GWAS analysis of nut quality traits important to pecan (Carya illinoinensis) breeding. Plant and Animal Genome Conference. San Diego,CA;12-17Jan2024.

Interpretive Summary:

Technical Abstract: Identifying the genetics associated with nut quality in pecan is critical to advancing pecan breeding with genomic selection methodologies. Yet, marker trait associations for only four traits have been published to date. A population genetic diversity re-sequence panel was chosen that included 745 pecan accessions and 137 hickory and hybrid accessions from the USDA ARS National Collection of Genetic Resources for Carya in College Station, TX. Phenotypic measurements and genotypic assessments were conducted on the panel to create marker trait associations. Sixteen morphological nut quality traits related to nut size, shape, volume, kernel fill, and kernel color were measured from 1988-2022 on subsets of 5 nuts from each accession in this panel. Sampling was not uniform across years, resulting in a sparse phenotype data matrix. This panel was sequenced with Illumina 150bp PE short reads at ~30-50x coverage and 402M SNPs were called against the 87MX3-2.11 reference genome. A GWAS analysis was performed using the R package 'ASRgwas', which used in conjunction with 'ASReml-R' 4.2 (VSNi International Ltd). Of the 16 nut quality traits tested, significant marker-trait associations (MTAs) were identified for nut length, nut density, kernel fuzz percentage, percentage packing material trapped in the kernel dorsal grooves, and nut roundness. A total of 12 MTA loci were identified, with candidate gene functions involved in lipid metabolism, oxidation reduction, biotic and abiotic stress responses, and abscisic acid synthesis. Our results provide a foundation for implementing genomic selection for nut quality and accelerating pecan breeding.