A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome

Li, Xuehui; Wei, Yanling; Acharya, Ananta; Jiang, Qingzhen; Kang, Junmei; Brummer, E. Charles

doi:10.1534/g3.114.012245

**A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome**

Journal Article · Thu Aug 21 00:00:00 EDT 2014 · G3

DOI:https://doi.org/10.1534/g3.114.012245· OSTI ID:1627951

Li, Xuehui ^[1]; Wei, Yanling ^[2]; Acharya, Ananta ^[2]; Jiang, Qingzhen ^[2]; Kang, Junmei ^[3]; Brummer, E. Charles ^[4]

The Samuel Roberts Noble Foundation, Ardmore, OK (United States); DOE/OSTI
The Samuel Roberts Noble Foundation, Ardmore, OK (United States)
Chinese Academy of Agricultural Science, Beijing (China)[
University of California, Davis, CA (United States)

A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F₁ population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa.

View Accepted Manuscript (DOE)

Research Organization:: University of California, Davis, CA (United States)

Sponsoring Organization:: China Scholarship Council; Samuel Roberts Noble Foundation; US Department of Agriculture; USDOE

OSTI ID:: 1627951

Journal Information:: G3, Journal Name: G3 Journal Issue: 10 Vol. 4; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
autotetraploid alfalfa
genetic linkage map
genotyping-by-sequencing