Phenotypic diversity and population structure of pecan (Carya illinoinensis) collections reveals geographic patterns

Authors: Wang, Xinwang; STEIN, LARRY - Texas A&M Agrilife; BLACK, MARK - Texas A&M Agrilife; Kubenka, Keith; RANDALL, JENNIFER - New Mexico State University; DING, CHEN - Auburn University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/6/2024
Publication Date: 8/10/2024
Citation: Wang, X., Stein, L., Black, M., Kubenka, K.A., Randall, J., Ding, C. 2024. Phenotypic diversity and population structure of pecan (Carya illinoinensis) collections reveals geographic patterns. Horticulture Research. 14(2024). Article e18592. https://doi.org/10.1038/s41598-024-69521-1.
DOI: https://doi.org/10.1038/s41598-024-69521-1

Interpretive Summary: Pecan is an important nut crop in the U.S.; however, it undergoes a long juvenile growth period before reaching nut production. The use of an appropriate rootstock can significantly shorten the time it takes for a pecan seedling to become a mature tree capable of fruiting. However, the breeding and selection of suitable pecan rootstocks face various challenges, including rootstock and scion interactions, rootstock adaptation to soil environments, disease and insect resistance, and growth habits, among others. This research utilized next-generation sequencing technology and identified several potential genomic variations associated with key growth traits during rootstock evaluation. These findings hold promise for guiding future rootstock breeding and selection efforts.

Technical Abstract: The grafting of pecan onto a desirable rootstock is a crucial practice in a well-established orchard, offering numerous benefits such as reducing the time to bear fruit, increasing nut yields, and enhancing the quality of the nutmeat. By grafting pecan varieties onto improved rootstocks, the risk of disease-related losses in nut production can be minimized, replanting becomes possible, and overall competitiveness is improved. However, the breeding and selection of pecan rootstocks face certain challenges, including significant maternal inheritance, environmental adaptation, and resistance to diseases. In this project, we aimed to evaluate various current and potential rootstocks from a diverse pecan collection grown in an area infested with Phymatotrichopsis omnivore, which causes cotton root rot disease. We examined 550 open-pollinated seedlings derived from 26 pecan provenances including natives and cultivars originating from Mexico and the U.S., which are maintained in the USDA Pecan Provenance orchard. Our objective was to estimate the population structure using these seedlings. To achieve this, we performed genome-wide association studies (GWAS) using standard Illumina protocols. The analysis revealed distinct population structures based on geographical origins and pedigree relationships. Furthermore, we investigated the associations between specific traits and single nucleotide polymorphism (SNP) markers through GWAS. As a result, we discovered 47 SNPs that exhibited significant associations with traits such as plant height, stem diameter, and terminal-most bud. By mapping these SNPs, we identified nine corresponding genes located on pecan chromosomes 1, 3, 8, 10, and 12, which play roles in regulating plant growth (e.g., plant height and trunk diameter) or flower development (e.g., terminal-most bud). However, we did not find any significant SNPs associated with reactions to cotton root rot. We discussed the variation in population structure, which can be attributed to factors such as population size, parentage or pollen source, and geographical origin. This study presents potential genetic tools that can be utilized in the breeding and selection of pecan rootstocks, enabling the development of improved varieties with enhanced traits and disease resistance.