Abstract
Pecan (Carya illinoinensis) is an outcrossing, highly heterozygous, and slow-to-mature tree native to North America. In order to better understand cultivar characteristics, appreciate regional adaptation, and improve selection in pecan breeding programs, improved genomic tools that are cost-effective and capable of high-throughput screening are necessary. A diverse panel of 108 cultivars and accessions from the National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya) was selected to represent regionally adapted native pecans, controlled cross progeny and their parents, selected wild relative species, and interspecific hybrids between those species and pecans. We implemented a genotyping-by-sequencing (GBS) technique to discover 87,446 informative single nucleotide polymorphisms (SNPs) throughout the pecan genome. SNPs were used to develop genomic profiles to confirm, refute, or inform questions of cultivar origin. Native accessions show strong genetic relationships by geographic region of origin. Matrices were developed to facilitate evaluation of pedigree relationships between cultivars. A genome-wide association study (GWAS) was performed to discover 17 SNPs from a contiguous region significantly associated with the expression of the simply inherited trait controlling flowering type (dichogamy). The information, techniques, and resources developed will benefit the pecan community by improving the ability to characterize germplasm and use marker data for marker-assisted breeding. This should reduce breeding time by facilitating more informed and efficient selection of parents and progeny.
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Acknowledgements
This work was supported by the United States Department of Agriculture Agricultural Research Service (USDA ARS) CRIS project 6202-21000-036-00D (Management and Characterization of Pecan Genetics Resources and Related Wild Populations), USDA ARS CRIS project 6202-21000-035-00D (Pecan Improvement Through Breeding and Genetics), Specific Cooperative Agreement 58-6202-1-201 (Developing Molecular Markers for Carya), Specific Cooperative Agreement 58-3091-5-031 (Genomic Markers for Carya), USDA Hatch funds, and USDA-SCRI 58-6042-6009 (Coordinated Development of Genetic Tools for Pecan). The authors wish to thank Ms. Natalie Patterson for help in pecan DNA extraction and Illumina template preparation and Ms. Rory Tucker for help in DNA extraction protocol modification. Illumina sequencing was provided by Texas A&M AgriLife Research Genomics and Bioinformatics Services. The authors also thank Linwood Nursery for providing ramets of their proprietary clones. Questions regarding living inventories should be directed to Dr. L.J. Grauke at LJ.Grauke@ars.usda.gov.
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L.J. Grauke designed the diversity panel and contributed data regarding each accession. Nolan Bentley developed the modified pecan DNA extraction protocol. Patricia Klein analyzed and generated SNP calls from the sequence data. Nolan Bentley wrote the R scripts and performed the downstream analyses of the SNP data. Nolan Bentley wrote the manuscript with revisions and contributions to the interpretation from L.J. Grauke and Patricia Klein.
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Table S1
Full calls and counts file for 87,446 SNPs (XLSX 126375 kb)
Table S2
Subset calls and counts file of the 40,586 SNPs used in the KGD and genetic distance analyses (XLSX 59027 kb)
Table S3
KGD relatedness value matrix (XLSX 138 kb)
Table S4
Tamura-Nei genetic distance value matrix (XLSX 124 kb)
Fig. S1
Two-dimensional histogram visualizing the distribution of the average absolute value of the difference in z-score adjusted read depths between adjacent SNPs on the same contig as a function of the bp difference in position measured between the SNPs being compared. The cyan bar shows the maximum value used to group SNPs if they were within 125 bp of each other and likely to represent the same mapped sequence associated with one side of a restriction enzyme site. Each square is a 1 bp difference wide and 0.016 y-unit tall bin with color indicating how many of 54,620 SNP comparisons shown are within its range (PNG 35 kb)
Fig. S2
PCA of KGD relatedness values between samples of pecan (right-side), bitternut hickory (C. cordiformis) (left-side), and bitternut x pecan interspecific hybrids (middle). Northern pecans include samples from MO, IL, IN, and KY. Intermediate pecans include OK and KS. The Mexican pecan is from Oaxaca, MX. San Felipe and Evers show evidence of admixture between Texan, Mexican, and Northern and Texan and Mexican germplasm, respectively. The two interspecific crosses cluster between the bitternut accession and the native pecan cluster that best matched that of their pecan parent (PDF 6 kb)
Fig. S3
Compilation and description of the historical documentation for Longfellow (PDF 2051 kb)
Data archiving statement
The sequences generated in this study have been submitted to the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under the BioProject number PRJNA413769.
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Bentley, N., Grauke, L.J. & Klein, P. Genotyping by sequencing (GBS) and SNP marker analysis of diverse accessions of pecan (Carya illinoinensis). Tree Genetics & Genomes 15, 8 (2019). https://doi.org/10.1007/s11295-018-1314-5
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DOI: https://doi.org/10.1007/s11295-018-1314-5