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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 #384669
Research Project: Pecan Breeding, Genomics, and Genetic Resource Management

Location: Crop Germplasm Research

Title: Development of SNP and SSR markers in pecan cultivars

Author
item Wang, Xinwang
item Kubenka, Keith
item Grauke, Larry

Submitted to: American Society of Horticulture Science Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 7/9/2021
Publication Date: 8/9/2021
Citation: Wang, X., Kubenka, K.A., Grauke, L.J. 2021. Development of SNP and SSR markers in pecan cultivars. American Society of Horticulture Science Meeting. Denver,CO;05-09Aug2021.

Interpretive Summary:

Technical Abstract: Short simple repeat sequences, or microsatellites (SSRs) are highly conservative motifs in an organism's genome. SSR markers have been widely applied for DNA profiling such as kinship (parentage and hybrid) and forensic identification, genetic linkage, population structure, population diversity. SSRs in pecan have been characterized with a certain number of markers in population diversity. More SSR markers are required to accurately address population dynamic diversity among Carya and its relative species. Pecan (Carya illinoinensis) is the major commercial planted nut tree among Carya species. Long juvenility, large tree size, and heterozygosity due to out-breeding hamper genomic characterization of this species. We sequenced Restriction-site Associated DNA (RAD) from nine pecan cultivar genomes. In total, 87.7M useful short reads with an average length of 45.91 bp, equivalent to about 5x pecan genomes were produced from four restriction enzyme-digested RAD libraries. Sequences were assembled into a total of 64,388 contigs N50 with an average length of 269 bp. Cultivar 'Wichita' generated the most contigs (10,455) and 'Sumner' the fewest (5,441). Contigs were mapped to two previously sequenced pecan cultivar scaffolds (87MX3-2.11 and 'Pawnee'), generating 78,264 and 56,047 SNP markers, respectively. Overall, the SNP variation among pecan cultivars has no significant difference, but apparently depends on their genetic/geographic distance from the reference genome. Contigs were also mined to discover 4,698 SSR motifs (di-nucleotides or longer), with 3,014 (64.2%) allowing design of SSR primers. In addition, of the four restriction enzymes, SbfI generated the highest number (41.6M) of useful reads from nine cultivars, of which approximately 18 M reads (43%) were assembled, followed by FseI and NotI. AscI showed the lowest numbers of reads and fewest SNP. The rates of SSR discovery from four RAD libraries showed the same trend with SNP discovery. Based on the preliminary results, SbfI was the optimal enzyme for RAD-based marker discovery in pecan. This study provides not only useful molecular markers for marker-assisted selection, population association mapping and genotyping, but a strategy for pecan whole genome sequencing and subsequently gene discovery.