Molecular Breeding

, Volume 29, Issue 4, pp 951–962 | Cite as

The strategy and potential utilization of temperate germplasm for tropical germplasm improvement: a case study of maize (Zea mays L.)

Article

Abstract

The organization of maize (Zea mays L.) germplasm into genetically divergent heterotic groups is the foundation of a successful hybrid maize breeding program. In this study, 94 CIMMYT maize lines (CMLs) and 54 United States germplasm enhancement of maize (GEM) lines were assembled and characterized using 1,266 single nucleotide polymorphisms (SNPs) with high quality. Based on principal component analysis (PCA), the GEM lines and CMLs were clearly separated. In the GEM lines, there were two groups classified by PCA corresponding to the heterotic groups “stiff stalk” and “non-stiff stalk”. CMLs did not form obvious subgroups by PCA. The allelic frequency of each SNP differed in GEM lines and CMLs. In total, 3.6% alleles (46/1,266) of CMLs are absent in GEM lines and 4.4% alleles (56/1,266) of GEM lines are absent in CMLs. The performance of F1 plants (n = 654) produced by crossing between different groups based on pedigree information was evaluated at the breeding nurseries of two CIMMYT stations. Genomic estimated phenotypic values of plant height and days to anthesis for a testing set of 45 F1 crosses were predicted based on the training data of 600 F1 crosses using a best linear unbiased prediction method. The prediction accuracy benefitted from the adoption of the markers associated with quantitative trait loci for both traits; however, it does not necessarily increase with an increase in marker density. It is suggested that genomic selection combined with association analysis could improve prediction efficiency and reduce cost. For hybrid maize breeding in the tropics, incorporating GEM lines which have unique alleles and clear heterotic patterns into tropically adapted lines could be beneficial for enhancing heterosis in grain yields.

Keywords

Heterotic groups Association analysis Genomic selection SNP 

Abbreviations

AF

Agua Fria

ANOVA

Analysis of variance

BLUP

Best linear unbiased prediction

CIMMYT

International Maize and Wheat Improvement Center

CML

CIMMYT maize line

crtRB1

β-Carotene hydroxylase

DA

Days to anthesis

GCA

General combining ability

GEM

Germplasm enhancement of maize

GWAS

Genome-wide association study

ISU

Iowa State University

LAMP

Latin American Maize Project

MAF

Minor allele frequency

MAS

Marker-assisted selection

NCU

North Carolina University

NSS

Non-stiff stalk

OPA

Oligo pool assay

PCA

Principal component analysis

SS

Stiff stalk

TL

Tlaltizapán

Supplementary material

11032_2011_9696_MOESM1_ESM.ppt (126 kb)
Fig. S1 Distribution of allelic frequency difference between germplasm enhancement of maize (GEM) and CIMMYT maize lines (CMLs). Supplementary material 1 (PPT 126 kb)
11032_2011_9696_MOESM2_ESM.ppt (120 kb)
Fig. S2 Distribution of kinship relations between any two lines in both 148 inbred lines and 654 F1s. GEM = Germplasm enhancement of maize; CML = CIMMYT maize line. Supplementary material 2 (PPT 120 kb)
11032_2011_9696_MOESM3_ESM.ppt (658 kb)
Fig. S3 Quantile–quantile plots of −log10(P) from association analysis based on a 148 inbred lines and b 654 F1s for days to anthesis (DA), and plant height (PH). The black line is the expected line under the null distribution. Under the assumption that there are few true associations, the observed P values are expected to nearly follow the expected P values. The deviations from the expectation demonstrate that the statistical analysis may cause spurious associations. Supplementary material 3 (PPT 657 kb)
11032_2011_9696_MOESM4_ESM.xls (42 kb)
Supplementary material 4 (XLS 42 kb)
11032_2011_9696_MOESM5_ESM.xls (64 kb)
Supplementary material 5 (XLS 64 kb)
11032_2011_9696_MOESM6_ESM.doc (28 kb)
Supplementary material 6 (DOC 28 kb)
11032_2011_9696_MOESM7_ESM.xls (72 kb)
Supplementary material 7 (XLS 72 kb)

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.International Maize and Wheat Improvement Center (CIMMYT)Mexico, D.F.Mexico
  2. 2.National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
  3. 3.National Maize Improvement CenterChina Agricultural UniversityBeijingChina
  4. 4.Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic ImprovementChinese Academy of Agricultural SciencesBeijingChina

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