A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize

Perez-Limon, Sergio; Li, Meng; Cintora-Martinez, G Carolina; Aguilar-Rangel, M. Rocío; Salazar-Vidal, M. Nancy; González‐Segovia, Eric; Blöcher-Juárez, Karla; Guerrero-Zavala, Alejandro; Barrales-Gamez, Benjamin; Carcaño-Macias, Jessica; Costich, Denise E.; Nieto-Sotelo, J.; Vega, Octavio Martínez de la; Simpson, June; Ross‐Ibarra, Jeffrey; Flint-García, Sherry; Diaz‐Garcia, Luis; Rellán‐Álvarez, Rubén; Sawers, Ruairidh J. H.

doi:10.1093/g3journal/jkab447

Cited by 12 publications

(11 citation statements)

References 113 publications

(172 reference statements)

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“…To further characterize the genetic architecture of phospholipid biosynthesis in highland maize, we developed a recombinant inbred line (RIL) BC1S5 population derived from a cross between the temperate inbred line B73 and the Mexican highland landrace Palomero Toluqueño (PT), using B73 as the recurrent parent (75% B73, 25% PT) (54).…”

Section: Resultsmentioning

confidence: 99%

“…The diversity panels and mapping populations used in this manuscript for population genetics measures of selection, QTL mapping and G x E analysis have been described previously by (19), (15), (44), (41) and (50). Lipidomics analysis were performed with high resolution mass spectrometry UPLC-MS. Mutant alleles of HPC1 were obtained using CRISPR-CAS9 editing.…”

Section: Methodsmentioning

confidence: 99%

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An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

Rodríguez-Zapata

Barnes

Blöcher-Juárez³

et al. 2021

Preprint

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After domestication from lowland teosinte parviglumis (Zea mays ssp. parviglumis) in the warm Mexican southwest, maize (Zea mays ssp. mays) colonized the highlands of Mexico and South America. In the highlands, maize was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature, low phosphorus availability and have also been suggested to influence flowering time. Here, we combined linkage mapping analysis with genome scans to identify High PhosphatidylCholine 1 (HPC1), a gene which encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The HPC1 variant we identified in highland maize results in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we show that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from Northern US, Canada and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

Rodríguez-Zapata

Barnes

Blöcher-Juárez³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Section: Resultsmentioning

confidence: 99%

“…The diversity panels and mapping populations used in this paper for population genetics measures of selection, QTL mapping, and G × E analysis have been described previously by refs. 15 , 19 , 41 , 44 , and 50 . Lipidomics analyses were performed with high-resolution mass spectrometry UPLC-MS (Ultra Performance Liquid Chromatography - Mass Spectrometry).…”

Section: Methodsmentioning

confidence: 99%

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

Barnes

Rodríguez-Zapata

Blöcher-Juárez

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.

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“…Maize has many advantages over other model organisms including the ease of creating controlled crosses and inbreds, extreme genetic diversity, easy to measure phenotypes, and a rich set of genetic and genomic resources [ 5 , 6 ]. Diverse germplasms are available around the world, for example through the USDA-ARS, National Genetic Resources Program ( https://www.ars-grin.gov/ ) and the International Maize and Wheat Improvement Center (CIMMYT - Mexico) [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Co-expression pan-network reveals genes involved in complex traits within maize pan-genome

2022

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Background With the advances in the high throughput next generation sequencing technologies, genome-wide association studies (GWAS) have identified a large set of variants associated with complex phenotypic traits at a very fine scale. Despite the progress in GWAS, identification of genotype-phenotype relationship remains challenging in maize due to its nature with dozens of variants controlling the same trait. As the causal variations results in the change in expression, gene expression analyses carry a pivotal role in unraveling the transcriptional regulatory mechanisms behind the phenotypes. Results To address these challenges, we incorporated the gene expression and GWAS-driven traits to extend the knowledge of genotype-phenotype relationships and transcriptional regulatory mechanisms behind the phenotypes. We constructed a large collection of gene co-expression networks and identified more than 2 million co-expressing gene pairs in the GWAS-driven pan-network which contains all the gene-pairs in individual genomes of the nested association mapping (NAM) population. We defined four sub-categories for the pan-network: (1) core-network contains the highest represented ~ 1% of the gene-pairs, (2) near-core network contains the next highest represented 1–5% of the gene-pairs, (3) private-network contains ~ 50% of the gene pairs that are unique to individual genomes, and (4) the dispensable-network contains the remaining 50–95% of the gene-pairs in the maize pan-genome. Strikingly, the private-network contained almost all the genes in the pan-network but lacked half of the interactions. We performed gene ontology (GO) enrichment analysis for the pan-, core-, and private- networks and compared the contributions of variants overlapping with genes and promoters to the GWAS-driven pan-network. Conclusions Gene co-expression networks revealed meaningful information about groups of co-regulated genes that play a central role in regulatory processes. Pan-network approach enabled us to visualize the global view of the gene regulatory network for the studied system that could not be well inferred by the core-network alone.

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A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize

Cited by 12 publications

References 113 publications

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

Co-expression pan-network reveals genes involved in complex traits within maize pan-genome

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