Development of a Next-Generation NIL Library in Arabidopsis Thaliana for Dissecting Complex Traits

dc.contributor.utaustinauthorJuenger, Thomas E.en_US
dc.creatorFletcher, Richard S.en_US
dc.creatorMullen, Jack L.en_US
dc.creatorYoder, Sethen_US
dc.creatorBauerle, William L.en_US
dc.creatorReuning, Gretchenen_US
dc.creatorSen, Saunaken_US
dc.creatorMeyer, Elien_US
dc.creatorJuenger, Thomas E.en_US
dc.creatorMcKay, John K.en_US
dc.description.abstractThe identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery. Results: In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait. Conclusions: The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.en_US
dc.description.departmentIntegrative Biologyen_US
dc.description.sponsorshipNSF DEB-1022196, DEB-0618302, DEB-0618347, IOS-09221457en_US
dc.identifier.citationFletcher, Richard S., Jack L. Mullen, Seth Yoder, William L. Bauerle, Gretchen Reuning, Saunak Sen, Eli Meyer, Thomas E. Juenger, and John K. McKay. "Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits." BMC genomics, Vol. 14, No. 1 (Sep., 2013): 655.en_US
dc.relation.ispartofserialBMC Genomicsen_US
dc.rightsAdministrative deposit of works to Texas ScholarWorks: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access or the publisher allows a PDF version of the article to be freely posted online. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en_US
dc.subjectquantitative trait locien_US
dc.subjectstomatal conductanceen_US
dc.subjectheterogeneous inbred familyen_US
dc.subjectnatural genetic-variationen_US
dc.subjectstomatal conductanceen_US
dc.subjectmicrosatellite locien_US
dc.subjectmapping populationen_US
dc.subjectdrought adaptationen_US
dc.subjectlinkage mapen_US
dc.subjectbiotechnology & applied microbiologyen_US
dc.subjectgenetics & heredityen_US
dc.titleDevelopment of a Next-Generation NIL Library in Arabidopsis Thaliana for Dissecting Complex Traitsen_US
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