Linkage mapping and QTL analysis of pecan ( Carya illinoinensis ) full-siblings using genotyping-by-sequencing
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ORIGINAL ARTICLE
Linkage mapping and QTL analysis of pecan (Carya illinoinensis) full-siblings using genotyping-by-sequencing Nolan Bentley 1 & L. J. Grauke 2,3 & Erin Ruhlman 1 & Robert R. Klein 3 & Keith Kubenka 2,3 & Xinwang Wang 2,3 & Patricia Klein 1 Received: 24 April 2020 / Revised: 5 October 2020 / Accepted: 28 October 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Pecan (Carya illinoinensis) is a nut-producing tree native to North America grown for its culinary, ornamental, and lumber characteristics. A newly developed chromosome-scale reference genome for pecan was used to create genotyping-by-sequencing (GBS)-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 1376.4 cM and 1463.1 cM for ‘Elliott’ and ‘VC1-68’, respectively. These markers, plus an additional 1096 intercross markers, were used to create a 1557.8-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 of observations. 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. In addition, the major budbreak QTL coincident in pecan and English walnut may represent a conserved mechanism effecting budbreak across the Juglandaceae providing critical knowledge for future investigations of variability in phenology. Keywords GBS . Mapping . QTL . Pecan . Carya . Breeding
Introduction Pecan (Carya illinoinensis) is a North American perennial tree cultivated for its culinary, ornamental, and lumber uses. Pecan is the most economically significant member of the Carya
Nolan Bentley and L. J. Grauke are co-first authors Communicated by E. Dirlewanger * Patricia Klein [email protected] 1
Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
2
National Collection of Genetic Resources for Pecans and Hickories, USDA ARS Pecan Breeding and Genetics, 10200 FM 50, Somerville, TX 77879, USA
3
United States Department of Agriculture-Agriculture Research Service, Plains Area, Southern Plains Agricultural Research Center, College Station, TX 77845, USA
genus (Grauke et al. 2016; Thompson and Grauke 1991). From 2015 to 2018, approximately 121,067 metric tons of kernels per year was produced worldwide with over 90% being grown in the USA and Mexico (INC 2015; 2016; 2017; 2018). While native pecan stands are still utilized, from 2017 to 2019 graf
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