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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #347154
Title: Identification of pecan scab resistance gene candidates in a pecan provenance collection using a combined bulked segregant analysis and genotyping by sequencing approach

Author
item ALARCON, YANINA - Noble Research Institute
item Bock, Clive
item WOOD, BRUCE - Retired ARS Employee
item ROHLA, CHARLES - Noble Research Institute
item MONTEROS, MARIA - Noble Research Institute

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/24/2017
Publication Date: 6/24/2017
Citation: Alarcon, Y., Bock, C.H., Wood, B.W., Rohla, C., Monteros, M. 2017. Identification of pecan scab resistance gene candidates in a pecan provenance collection using a combined bulked segregant analysis and genotyping by sequencing approach. American Society of Plant Biologists Annual Meeting. p. 129-130.

Interpretive Summary:

Technical Abstract: Pecan [Carya illinoinensis (Wangenh.) K. Koch] is an important horticultural crop in the USA worth over $560 million in 2015. Pecan is a diploid species endemic to the Mississippi River Valley. Pecan scab is caused by the fungus Fusicladium effusum and infection causes losses in nut yield and quality. Fungicide applications may help mitigate the disease effects but these are not a viable long-term strategies due to the large size of the trees, the number of applications needed, the costs associated with fungicide spraying and potential breakdown of fungicide activity. Genomic resources generated by next-generation sequencing technologies and molecular markers can be used to discover key loci associated with pecan scab resistance. A pecan provenance collection representing the natural range of pecan growth was rated for scab response annually in the field for three years. Bulked segregant analysis (BSA) and genotype-by sequencing (GBS) resulted in the identification of 3,603 SNPs between pecan scab susceptible and tolerant bulks from six provenances. SNPs in 101 candidate genes for scab resistance were identified between contrasting bulks. The candidate genes were identified based on the annotation from the black walnut genome and include leucine-rich repeat receptor like protein kinases, chitinases, cysteine-rich receptor-like protein kinases, MATE efflux family proteins, and peroxidases among others. SNP validation using high-resolution melting analysis was performed in individual trees from the twelve bulks used for GBS. Ongoing work focuses on further evaluating the target disease resistance candidate genes and exploring their role in a mapping population segregating for scab susceptibility. Further evaluating transcriptome changes of susceptible and resistant tress in response to scab infection can provide additional insights on the key genes critical for scab disease resistance.