Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations

Тип публикации: статья из журнала

Год издания: 2013

Идентификатор DOI: 10.1007/s11295-013-0624-x

Ключевые слова: Association mapping, Adaptive traits, Breeding, Genomic variation, Genome-wide linkage disequilibrium, Loblolly pine, Pinus taeda, Population structure, SNPs, Adaptive traits, Association mapping, Breeding, Genome-wide linkage disequilibrium, Genomic variation, Loblolly pine, Pinus taeda, Population structure, SNPs, Pinus taeda

Аннотация: First-generation selection (FGS) and second-generation selection (SGS) breeding populations of loblolly pine from east Texas were studied to estimate the genetic diversity, population structure, linkage disequilibrium (LD), signatures of selection and association of breeding traits with a genome-wide panel of 4,264 single nucleotide polymorphisms (SNPs). Relatively high levels of observed (H (o) = 0.178-0.198) and expected (H (e) = 0.180-0.198) heterozygosities were observed in all populations. The amount of inbreeding was very low with many populations exhibiting a slight excess of heterozygotes. The population structure was weak, but F (ST) indicated more pronounced differentiation in the SGS populations. As expected for outcrossing natural populations, the genome-wide LD was low, but marker density was insufficient to deduce the decay rate. Numerous associations were found between various phenotypic traits and SNPs, but only a few remained significant after false positive correction. Signatures of diversifying and balancing selection were found in markers representing important biological functions. These results present the first step in the application of marker-assisted selection (MAS) to the Western Gulf Forest Tree Improvement Program (WGFTIP) for loblolly pine and will contribute to the knowledgebase necessary for genomic selection technology.

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Издание

Журнал: TREE GENETICS & GENOMES

Выпуск журнала: Vol. 9, Is. 5

Номера страниц: 1161-1178

ISSN журнала: 16142942

Место издания: HEIDELBERG

Издатель: SPRINGER HEIDELBERG

Авторы

  • Chhatre Vikram E. (Texas A&M Univ, Grad Program Genet, College Stn, TX 77843 USA; Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA)
  • Byram Thomas D. (Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA; Texas Forest Serv, Western Gulf Forest Tree Improvement Program, College Stn, TX 77843 USA)
  • Neale David B. (Univ Calif Davis, Dept Plant Sci, Davis, CA 95616 USA)
  • Wegrzyn Jill L. (Univ Calif Davis, Dept Plant Sci, Davis, CA 95616 USA)
  • Krutovsky Konstantin V. (Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA; Univ Gottingen, Busgen Inst, Dept Forest Genet & Forest Tree Breeding, D-37077 Gottingen, Germany; Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia; Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119333, Russia)

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