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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 #374166

Research Project: Enhancement of Elite Sorghum Germplasm through Introgression Breeding and Analysis of Traits Critical to Hybrid Development

Location: Crop Germplasm Research

Title: Linkage mapping and QTL analysis of pecan (Carya illinoinensis) full-siblings using genotyping-by-sequencing

item BENTLEY, NOLAN - Texas A&M University
item Grauke, Larry
item RUHLMAN, ERIN - Texas A&M University
item Klein, Robert - Bob
item Kubenka, Keith
item Wang, Xinwang
item KLEIN, PATRICIA - Texas A&M University

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2020
Publication Date: 11/10/2020
Citation: Bentley, N., Grauke, L.J., Ruhlman, E., Klein, R.R., Kubenka, K.A., Wang, X., Klein, P. 2020. Linkage mapping and QTL analysis of pecan (Carya illinoinensis) full-siblings using genotyping-by-sequencing. Tree Genetics and Genomes. 16. Article 83.

Interpretive Summary: Pecan is a nut producing tree native to North America grown for its culinary, ornamental, and lumber characteristics. Pecan is the most economically important member of the Carya genus, and improved cultivars comprised over 90% of the average value of the yearly pecan crop in the United States. The development of improved cultivars by conventional methodologies is challenging and because of this, a major goal of the USDA National Collection of Genetic Resources for Pecans and Hickories is to develop the genomic resources to accelerate the identification and release of superior pecan cultivars. This study developed genetic maps for pecan, and then utilized these maps to find regions of chromosomes that control resistance to an important fungal disease and springtime budbreak. The genomic tools presented in the study, when used with the pecan orchard for which the tools were developed, represent a valuable resource for future genetic investigations by USDA scientists and their collaborators.

Technical Abstract: A newly developed chromosome-scale reference genome for pecan was used to create genotyping-by-sequencing based high-density genetic linkage maps of 151 full-sibling progeny of Elliott and VC1-68. These maps incorporate 6142 SNPs segregating in a testcross pattern into 32 linkage groups representing the 16 chromosomes of pecan across the two parents. The average distance between markers was 0.46 cM and the two maps totaled 1376 cM and 1463 cM for Elliott and VC1-68, respectively. These markers, plus an additional 1096 intercross markers were used to create a 1558 cM pecan consensus genetic linkage map. Quantitative trait locus (QTL) analyses revealed 1 major and 2 minor effect QTL for budbreak and 1 minor effect QTL for pecan scab susceptibility. The major effect locus inherited from VC1-68 explained up to 30% of the variation in budbreak and appeared across 3 years. This QTL is syntenic to recently identified major effect QTL for budbreak in English walnut. The techniques reported herein, and the resulting genetic maps will facilitate future discoveries of valuable fruiting-trait loci as this pecan population completes the transition to sexual maturity.