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Distinct genetic architectures for phenotype means and plasticities in Zea mays.

ABSTRACT: Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2.5 million single-nucleotide polymorphisms. We show that across all traits the candidate genes for mean phenotype values and plasticity measures form structurally and functionally distinct groups. Such independent genetic control suggests that breeders will be able to select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both high mean phenotype values and levels of plasticity that are appropriate for the target performance environments.

SUBMITTER: Kusmec A

PROVIDER: S-EPMC6209453 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Distinct genetic architectures for phenotype means and plasticities in Zea mays.

Kusmec Aaron A Srinivasan Srikant S Nettleton Dan D Schnable Patrick S PS

Nature plants 20170904 9

Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grow ...[more]

PMID: 29150689

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Project description:BackgroundCold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their alleviation are shared or vary across genotypes. In this study we identify individual transcripts and groups of functionally related transcripts that consistently respond to cold and its alleviation. Genes that respond differently to temperature changes across genotypes may have limited functional importance. We investigate if these genes share functions, and if their genotype-specific gene expression levels change in magnitude or rank across temperatures.ResultsWe estimate transcript abundances from over 22,000 genes in two unrelated Zea mays inbred lines during and after cold temperature exposure. Genotype and temperature contribute to many genes' abundances. Past cold exposure affects many fewer genes. Genes up-regulated in cold encode many cytokinin glucoside biosynthesis enzymes, transcription factors, signalling molecules, and proteins involved in diverse environmental responses. After cold exposure, protease inhibitors and cuticular wax genes are newly up-regulated, and environmentally responsive genes continue to be up-regulated. Genes down-regulated in response to cold include many photosynthesis, translation, and DNA replication associated genes. After cold exposure, DNA replication and translation genes are still preferentially downregulated. Lignin and suberin biosynthesis are newly down-regulated. DNA replication, reactive oxygen species response, and anthocyanin biosynthesis genes have strong, genotype-specific temperature responses. The ranks of genotypes' transcript abundances often change across temperatures.ConclusionsWe report a large, core transcriptome response to cold and the alleviation of cold. In cold, many of the core suite of genes are up or downregulated to control plant growth and photosynthesis and limit cellular damage. In recovery, core responses are in part to prepare for future stress. Functionally related genes are consistently and greatly up-regulated in a single genotype in response to cold or its alleviation, suggesting positive selection has driven genotype-specific temperature responses in maize.

Project description:Maize (Zea mays L.) is an important source of carbohydrates and protein in the diet in sub-Saharan Africa. The objectives of this study were to (i) estimate general (GCA) and specific combining abilities (SCA) of 13 new quality protein maize (QPM) lines in a diallel under stress and non-stress conditions, (ii) compare observed and predicted performance of QPM hybrids, (iii) characterize genetic diversity among the 13 QPM lines using single nucleotide polymorphism (SNP) markers and assess the relationship between genetic distance and hybrid performance, and (iv) assess diversity and population structure in 116 new QPM inbred lines as compared to eight older tropical QPM lines and 15 non-QPM lines. The GCA and SCA effects were significant for most traits under optimal conditions, indicating that both additive and non-additive genetic effects were important for inheritance of the traits. Additive genetic effects appeared to govern inheritance of most traits under optimal conditions and across environments. Non-additive genetic effects were more important for inheritance of grain yield but additive effects controlled most agronomic traits under drought stress conditions. Inbred lines CKL08056, CKL07292, and CKL07001 had desirable GCA effects for grain yield across drought stress and non-stress conditions. Prediction efficiency for grain yield was highest under optimal conditions. The classification of 139 inbred lines with 95 SNPs generated six clusters, four of which contained 10 or fewer lines, and 16 lines of mixed co-ancestry. There was good agreement between Neighbor Joining dendrogram and Structure classification. The QPM lines used in the diallel were nearly uniformly spread throughout the dendrogram. There was no relationship between genetic distance and grain yield in either the optimal or stressed environments in this study. The genetic diversity in mid-altitude maize germplasm is ample, and the addition of the QPM germplasm did not increase it measurably.

Dataset Information

Distinct genetic architectures for phenotype means and plasticities in Zea mays.

Publications

Distinct genetic architectures for phenotype means and plasticities in Zea mays.

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