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Title: Fine mapping of the soybean aphid-resistance genes Rag6 and Rag3c from Glycine soja 85-32

item ZHANG, SHICHEN - Michigan State University
item ZHANG, ZHONGNAN - Michigan State University
item WEN, ZIXIANG - Michigan State University
item GU, CUIHUA - Michigan State University
item An, Yong-Qiang - Charles
item BALES, CARMILLE - Michigan State University
item DIFONZO, CHRIS - Michigan State University
item Song, Qijian
item WANG, DECHUN - Michigan State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/30/2017
Publication Date: 9/8/2017
Publication URL:
Citation: Zhang, S., Zhang, Z., Wen, Z., Gu, C., An, Y., Bales, C., DiFonzo, C., Song, Q., Wang, D. 2017. Fine mapping of the soybean aphid-resistance genes Rag6 and Rag3c from Glycine soja 85-32. Theoretical and Applied Genetics. 130(12):2601-2615.

Interpretive Summary: Soybean is the second largest crop in US with annual production of 107 million metric tons valued $34.5 billion. Soybean is grown for a variety of uses such as livestock feed, cooking oil, protein source and biodiesel. However, over the past decade, North American soybean production has been threatened by an invasive species, the soybean aphid that originated from Asia. Since its discovery in the Great Lakes region in 2000, soybean aphid has aggressively spread to all the major soybean producing areas in the United States and Canada. Host-plant resistance is a preferred approach to manage aphids. Having applied new genetic and next-generation DNA sequencing technologies, we defined two aphid-resistant genes (Rag6 and Rag3c) into two small DNA regions on soybean genome respectively, and identified candidate genes and gene mutations potentially responsible for the aphid resistance. Highly effective DNA markers were developed as well. The DNA markers and the candidate genes identified in this study will be significant resources to develop aphid resistant cultivars and understand molecular mechanism underlying the resistance.

Technical Abstract: The soybean aphid, an invasive species, has significantly threatened soybean production in North America since 2001. Host-plant resistance is known as an ideal management of aphids. Two novel aphid-resistant loci, Rag6 and Rag3c, from the Glycine soja accession 85-32, were previously detected in a 10.5 centiMorgan (cM)-interval on chromosome 8 and a 7.5 cM-interval on chromosome 16, respectively. Defining the exact genomic position of these two genes is critical for improving the effectiveness of marker-assisted selection for aphid resistance and for identification of the functional genes. To pinpoint the locations of Rag6 and Rag3c, four populations segregating for Rag6 and Rag3c were used to fine map these two genes in the soybean genome. With SNP markers developed from the whole genome re-sequencing data and the Illumina Infinium SoySNP50K iSelect BeadChip, Rag6 was refined to a 49-kb interval on chromosome 8 with the presence of four candidate genes, including three clustered nucleotide-binding site leucine-rich repeat (NBS-LRR) genes and an amine oxidase encoding gene; Rag3c was refined to a 150-kb interval on chromosome 16 with the presence of eleven candidate genes, two of which are a NBS-LRR gene and a lipase gene. Moreover, with whole genome exome-capture sequencing of the resistant source, structural variants were identified on the exons of the candidate genes of Rag6 and Rag3c. The closely linked SNP markers and the candidate gene information presented in this study will be significant resources for integrating Rag6 and Rag3c to elite cultivars and future gene functional studies.