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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Sunflower and Plant Biology Research » Research » Publications at this Location » Publication #323384
Title: SNP discovery and QTL mapping of Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing (GBS)

Author
item ZAHIRUL, TALUKDER - North Dakota State University
item Seiler, Gerald
item Song, Qijian
item MA, GUOJIA - North Dakota State University
item Qi, Lili

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/19/2016
Publication Date: 10/6/2016
Citation: Zahirul, T.I., Seiler, G.J., Song, Q., Ma, G., Qi, L. 2016. SNP discovery and QTL mapping of Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing (GBS). The Plant Genome. 9(3). doi:10.3835/plantgenome 2016.03.0035.

Interpretive Summary: Basal stalk rot (BSR) is a serious disease of sunflower (Helianthus annuus L.) causing significant yield reduction in the cool and humid areas of the world. Host resistance is the most effective method for controlling BSR disease caused by Sclerotinia sclerotiorum. Due to the lack of completely resistant source, breeding for BSR resistance relies on incorporating genetic factors from various partially tolerant breeding lines. Our understanding of the genetic basis of BSR resistance in sunflower is quite limited. In this study a mapping population was developed by crossing two BSR tolerant sunflower lines and grew the population in multiple locations and assessed BSR disease incidence in each of the genetic lines. The objective of the study was to determine the genomic location of the genes, commonly known as quantitative trait loci (QTL) that seemed to associate with BSR tolerance in the parental lines using genotyping-by-sequencing approach. Ten significant QTL were identified, four of them detected repeatedly across environments, each explaining between 18 and 36% of the phenotypic variance. Both the parents contributed QTL associated with elevated level of BSR tolerance. These findings will increase the efficiency of sunflower breeding programs through marker-assisted selection and help breeders select for cultivars with improved BSR resistance in their breeding programs.

Technical Abstract: Basal stalk rot (BSR) caused by the ascomycete fungus Sclerotinia sclerotiorum (Lib.) de Bary is a serious disease of sunflower (Helianthus annuus L.) in the cool and humid production areas of the world. Quantitative trait loci (QTL) for BSR resistance were identified in a sunflower recombinant inbred line (RIL) population derived from the cross HA 441/RHA 439. Genotyping-by-sequencing (GBS) approach was adapted to discover single-nucleotide polymorphism (SNP) markers and simultaneously genotyping the RIL population. A genetic linkage map was developed comprised of 1,049 SNP markers on 17 linkage groups spanning 1,431.05 cM. The RILs were tested in five environments (locations and/or years) for resistance to BSR. Quantitative trait loci were identified in each environment separately, with consensus reached on the number and precise position of the repeatedly mapped QTL across environments using a QTL-meta analysis. Ten significant QTL were identified; four were meta-QTL spanning within 15.27 cM on LG10, each explaining between 18 and 36% of the observed phenotypic variance. The remaining six significant QTL, two each on LGs 11 and 17 and one each on LGs 9 and 16 were identified in only one environment, each explaining between 9 and 26% of the phenotypic variance. Alleles conferring increased resistance were contributed by both parents. The potential utility of the important QTL in marker assisted selection (MAS) breeding was discussed and the SNP markers flanking these QTL were converted into allele-specific markers for immediate use.