A study of allelic diversity underlying flowering-time adaptation in maize landraces.
Landraces (traditional varieties) of domesticated species preserve useful genetic variation, yet they remain untapped due to the genetic linkage between the few useful alleles and hundreds of undesirable alleles. We integrated two approaches to characterize the diversity of 4,471 maize landraces. First, we mapped genomic regions controlling latitudinal and altitudinal adaptation and identified 1,498 genes. Second, we used F-one association mapping (FOAM) to map the genes that control flowering time, across 22 environments, and identified 1,005 genes. In total, we found that 61.4% of the single-nucleotide polymorphisms (SNPs) associated with altitude were also associated with flowering time. More than half of the SNPs associated with altitude were within large structural variants (inversions, centromeres and pericentromeric regions). The combined mapping results indicate that although floral regulatory network genes contribute substantially to field variation, over 90% of the contributing genes probably have indirect effects. Our dual strategy can be used to harness the landrace diversity of plants and animals.
School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA.
J Alberto
JA
Romero Navarro
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Martha
M
Willcox
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Juan
J
Burgueño
Institute for Genomic Diversity, Ithaca, New York, USA.
Cinta
C
Romay
School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA.
Kelly
K
Swarts
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Samuel
S
Trachsel
Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Campo Experimental Bajio, Celaya, México.
Ernesto
E
Preciado
Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Campo Experimental Bajio, Celaya, México.
Arturo
A
Terron
Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Campo Experimental Uruapan, Uruapan, México.
Humberto Vallejo
HV
Delgado
Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Campo Experimental Santiago Ixcuintla, Santiago Ixcuintla, México.
Victor
V
Vidal
Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Campo Experimental Norman E. Borlaug, Ciudad Obregón, México.
Alejandro
A
Ortega
Universidad Autonoma Agraria Antonio Narro, Torreon, México.
Armando Espinoza
AE
Banda
Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Campo Experimental Iguala, Iguala, México.
Noel Orlando Gómez
NO
Montiel
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Ivan
I
Ortiz-Monasterio
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Félix San
FS
Vicente
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Armando Guadarrama
AG
Espinoza
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Gary
G
Atlin
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Peter
P
Wenzl
International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México.
Sarah
http://orcid.org/0000-0003-2015-2450
S
Hearne
School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA.|Institute for Genomic Diversity, Ithaca, New York, USA.|US Department of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, New York, USA.
Edward S
http://orcid.org/0000-0002-3100-371X
ES
Buckler
D000064:Acclimatization / Q000235:genetics; D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D002874:Chromosome Mapping / Q000379:methods; D035264:Flowers / Q000235:genetics*; D008040:Genetic Linkage / Q000235:genetics; D005838:Genotype; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*