TY - JOUR
T1 - Germplasm architecture revealed through chromosomal effects for quantitative traits in maize
AU - Bernardo, Rex
AU - Thompson, Addie M.
N1 - Publisher Copyright:
© Crop Science Society of America.
PY - 2016/7
Y1 - 2016/7
N2 - Germplasm architecture refers to how favorable alleles for a given trait are distributed across the genome in a germplasm collection. Our objective was to assess germplasm architecture for quantitative traits among US maize (Zea mays L.) inbreds. A total of 271 inbreds were genotyped at 28,626 single nucleotide polymorphism (SNP) loci and phenotyped for anthesis date, plant height, starch and protein concentration, and resistance to northern corn leaf blight (NCLB, caused by Setosphaeria turcica). Chromosomal effects were calculated as the sum of the trait effects of SNP alleles carried on a specific chromosome by an inbred. The chromosomal effects were further decomposed into the mean effects of chromosomes, mean effects of inbreds, and chromosome × inbred effects. On average, none of the 10 maize chromosomes was particularly rich or poor in favorable quantitative trait locus (QTL) alleles. However, extreme values of chromosome × inbred effects often involved chromosomes 5 and 8 for anthesis date, chromosomes 1 and 5 for plant height, and chromosome 9 for protein concentration. Inbreds with one or two chromosomes deficient in favorable alleles were candidates for improvement via chromosome-substitution lines. Specific chromosomes for which each of five genetic backgrounds (B73, Mo17, Oh43, A321, and PH207) were rich or poor for unknown favorable alleles were also identified. Chromosomal effects varied widely even when prior association mapping in the same germplasm collection had failed to identify any QTL. Genomewide marker effects, particularly when partitioned into chromosomal effects, provide a simple way to dissect germplasm architecture for quantitative traits.
AB - Germplasm architecture refers to how favorable alleles for a given trait are distributed across the genome in a germplasm collection. Our objective was to assess germplasm architecture for quantitative traits among US maize (Zea mays L.) inbreds. A total of 271 inbreds were genotyped at 28,626 single nucleotide polymorphism (SNP) loci and phenotyped for anthesis date, plant height, starch and protein concentration, and resistance to northern corn leaf blight (NCLB, caused by Setosphaeria turcica). Chromosomal effects were calculated as the sum of the trait effects of SNP alleles carried on a specific chromosome by an inbred. The chromosomal effects were further decomposed into the mean effects of chromosomes, mean effects of inbreds, and chromosome × inbred effects. On average, none of the 10 maize chromosomes was particularly rich or poor in favorable quantitative trait locus (QTL) alleles. However, extreme values of chromosome × inbred effects often involved chromosomes 5 and 8 for anthesis date, chromosomes 1 and 5 for plant height, and chromosome 9 for protein concentration. Inbreds with one or two chromosomes deficient in favorable alleles were candidates for improvement via chromosome-substitution lines. Specific chromosomes for which each of five genetic backgrounds (B73, Mo17, Oh43, A321, and PH207) were rich or poor for unknown favorable alleles were also identified. Chromosomal effects varied widely even when prior association mapping in the same germplasm collection had failed to identify any QTL. Genomewide marker effects, particularly when partitioned into chromosomal effects, provide a simple way to dissect germplasm architecture for quantitative traits.
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U2 - 10.3835/plantgenome2016.03.0028
DO - 10.3835/plantgenome2016.03.0028
M3 - Article
C2 - 27898815
AN - SCOPUS:84978127554
SN - 1940-3372
VL - 9
JO - Plant Genome
JF - Plant Genome
IS - 2
ER -