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This article in TPG

  1. Vol. 4 No. 1, p. 24-35
    OPEN ACCESS
     
    Received: Sept 16, 2010
    Published: Mar, 2011


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doi:10.3835/plantgenome2010.09.0022

Association Mapping of Biomass Yield and Stem Composition in a Tetraploid Alfalfa Breeding Population

  1. Xuehui Li11,
  2. Yanling Wei11,
  3. Kenneth J. Moore,
  4. Réal Michaud,
  5. Donald R. Viands,
  6. Julie L. Hansen,
  7. Ananta Acharya and
  8. E. Charles Brummer 
  1. X. Li, Y. Wei, and E.C. Brummer, Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK 73401; K.J. Moore, Dep. of Agronomy, Iowa State Univ., Ames, IA 50011; R. Michaud, Agriculture and Agri-Food Canada, Ste. Foy, QC, Canada G1V 2J3; D.R. Viands and J. L. Hansen, Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14853. A. Acharya, Institute of Plant Breeding, Genetics, and Genomics, Univ. of Georgia, Athens, GA 30602.

Abstract

Alfalfa (Medicago sativa L.), an important forage crop that is also a potential biofuel crop, has advantages of high yield, high lignocellulose concentration in stems, and has low input costs. In this study, we investigated population structure and linkage disequilibrium (LD) patterns in a tetraploid alfalfa breeding population using genome-wide simple sequence repeat (SSR) markers and identified markers related to yield and cell wall composition by association mapping. No obvious population structure was found in our alfalfa breeding population, which could be due to the relatively narrow genetic base of the founders and/or due to two generations of random mating. We found significant LD (p < 0.001) between 61.5% of SSR marker pairs separated by less than 1 Mbp. The observed large extent of LD could be explained by the effect of bottlenecking and selection or the high mutation rates of SSR markers. Total marker heterozygosity was positively related to biomass yield in each of five environments, but no relationship was noted for stem composition traits. Of a total of 312 nonrare (frequency >10%) alleles across the 71 SSR markers, 15 showed strong association (p < 0.005) with yield in at least one of five environments, and most of the 15 alleles were identified in multiple environments. Only one allele showed strong association with acid detergent fiber (ADF) and one allele with acid detergent lignin (ADL). Alleles associated with traits could be directly applied in a breeding program using marker-assisted selection. However, based on our estimated LD level, we would need about 1000 markers to explore the whole alfalfa genome for association between markers and traits.

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