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. 2016 Jun 6;16(1):127.
doi: 10.1186/s12870-016-0816-2.

Association mapping for cold tolerance in two large maize inbred panels

Pedro Revilla  1 , Víctor Manuel Rodríguez  2 , Amando Ordás  2 , Renaud Rincent  3 , Alain Charcosset  3 , Catherine Giauffret  4 , Albrecht E Melchinger  5 , Chris-Carolin Schön  6 , Eva Bauer  6 , Thomas Altmann  7 , Dominique Brunel  8 , Jesús Moreno-González  9 , Laura Campo  9 , Milena Ouzunova  10 , Ángel Álvarez  11 , José Ignacio Ruíz de Galarreta  12 , Jacques Laborde  13 , Rosa Ana Malvar  2
Affiliations

Association mapping for cold tolerance in two large maize inbred panels

Pedro Revilla et al. BMC Plant Biol. .

Abstract

Background: Breeding for cold tolerance in maize promises to allow increasing growth area and production in temperate zones. The objective of this research was to conduct genome-wide association analyses (GWAS) in temperate maize inbred lines and to find strategies for pyramiding genes for cold tolerance. Two panels of 306 dent and 292 European flint maize inbred lines were evaluated per se and in testcrosses under cold and control conditions in a growth chamber. We recorded indirect measures for cold tolerance as the traits number of days from sowing to emergence, relative leaf chlorophyll content or quantum efficiency of photosystem II. Association mapping for identifying genes associated to cold tolerance in both panels was based on genotyping with 49,585 genome-wide single nucleotide polymorphism (SNP) markers.

Results: We found 275 significant associations, most of them in the inbreds evaluated per se, in the flint panel, and under control conditions. A few candidate genes coincided between the current research and previous reports. A total of 47 flint inbreds harbored the favorable alleles for six significant quantitative trait loci (QTL) detected for inbreds per se evaluated under cold conditions, four of them had also the favorable alleles for the main QTL detected from the testcrosses. Only four dent inbreds (EZ47, F924, NK807 and PHJ40) harbored the favorable alleles for three main QTL detected from the evaluation of the dent inbreds per se under cold conditions. There were more QTL in the flint panel and most of the QTL were associated with days to emergence and ΦPSII.

Conclusions: These results open new possibilities to genetically improve cold tolerance either with genome-wide selection or with marker assisted selection.

Keywords: Chilling; Cold tolerance; GWAS, Maize; QTL.

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Figures

Fig. 1
Fig. 1
Significant SNPs and QTL associated to cold tolerance traits in two association panels of maize. Inbred lines were evaluated per se (a) and in testcrosses (b) under control and cold conditions
Fig. 2
Fig. 2
GWAS results for early vigor in the Flint panel. The graph represents -log10(P-values) of the 35963 SNPs tested. The line shows the significant threshold of -log10(P-values)
Fig. 3
Fig. 3
Local LD, measured as rr values between pairs of SNPs (white, r 2 = 0; shades of gray = 0 < r2<, 1; black r2 = 1), and haplotype blocks for a 1.4 -kb genomic region that surrounds significant SNPs associated to cold tolerance traits in two association panels of maize inbred lines evaluated under control and cold conditions
See this image and copyright information in PMC

References

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