Phenotypic variation has been manipulated by humans during crop domestication, which occurred primarily between 3000 and 10000 years ago in the various centers of origin around the world. The process ...of domestication has profound consequences on crops, where the domesticate has moderately reduced genetic diversity relative to the wild ancestor across the genome, and severely reduced diversity for genes targeted by domestication. The question that remains is whether reduction in genetic diversity has affected crop production today. A case study in maize (Zea mays) demonstrates the application of understanding relationships between genetic diversity and phenotypic diversity in the wild ancestor and the domesticate. As an outcrossing species, maize has tremendous genetic variation. The complementary combination of genome-wide association mapping (GWAS) approaches, large HapMap data sets, and germplasm resources is leading to important discoveries of the relationship between genetic diversity and phenotypic variation and the impact of domestication on trait variation.
Crop improvement and the dissection of complex genetic traits require germplasm diversity. Although this necessary phenotypic variability exists in diverse maize, most research is conducted using a ...small subset of inbred lines. An association population of 302 lines is now available - a valuable research tool that captures a large proportion of the alleles in cultivated maize. Provided that appropriate statistical models correcting for population structure are included, this tool can be used in association analyses to provide high-resolution evaluation of multiple alleles. This study describes the population structure of the 302 lines, and investigates the relationship between population structure and various measures of phenotypic and breeding value. On average, our estimates of population structure account for 9.3% of phenotypic variation, roughly equivalent to a major quantitative trait locus (QTL), with a high of 35%. Inclusion of population structure in association models is critical to meaningful analyses. This new association population has the potential to identify QTL with small effects, which will aid in dissecting complex traits and in planning future projects to exploit the rich diversity present in maize.
Maize (Zea mays L. subsp. mays) is the most important crop in the United States, but maize food and distillation products often rely on varieties that are not bred explicitly for these purposes. ...Farmers targeting niche food grain markets have expressed interest in historical open‐pollinated varieties of maize, but few such populations are widely available, and even fewer are well‐characterized. We planted field trials of 76 open‐pollinated heirloom varieties available from seed catalogs and the United States Department of Agriculture germplasm collection along with four F1 hybrid cultivars. We measured 24 traits across 3 years and three locations to characterize the selected varieties and measure their phenotypic relationships. We identified a subset of 19 traits with heritability >0.5 and pairwise correlation coefficients not exceeding 0.9 for phenotypic analysis. Our results demonstrate that many historical accessions contain substantial genetic variation that should permit improvement from within‐population selection. Variety name and origin are often not useful indicators of phenotypic relationships or potential crop value, although Hickory King varieties have maintained their identity even following global dispersion. Cluster analysis identifies nine morphologically distinct groups within the varieties tested, which are largely in agreement with previously proposed landrace groupings. Our results suggest a complex intermixing of Southern Dents with other maize types, rather than a clear distinction between Southern Dents and Derived Southern Dents, however. Genetic analysis of larger samples of US open‐pollinated populations will help better define the natural classification of maize indigenous to the United States.
Core Ideas
Open‐pollinated maize populations have lower yield potential but unique agronomic and culinary qualities.
We evaluated maize open‐pollinated populations adapted to Southeastern United States to study their relationships.
We identified phenotypically distinct sub‐groups of previously named maize taxonomic groups.
We observed significant within‐population variation for all traits; these populations can be improved by breeding.
Populations with distinct ear and kernel traits and with acceptable agronomic performance were identified.
Stalk strength is an important trait in maize (Zea mays L.). Strong stalks reduce lodging and maximize harvestable yield. Studies show rind penetrometer resistance (RPR), or the force required to ...pierce a stalk rind with a spike, is a valid approximation of strength. We measured RPR across 4,692 recombinant inbreds (RILs) comprising the maize nested association mapping (NAM) panel derived from crosses of diverse inbreds to the inbred, B73. An intermated B73×Mo17 family (IBM) of 196 RILs and a panel of 2,453 diverse inbreds from the North Central Regional Plant Introduction Station (NCRPIS) were also evaluated. We measured RPR in three environments. Family-nested QTL were identified by joint-linkage mapping in the NAM panel. We also performed a genome-wide association study (GWAS) and genomic best linear unbiased prediction (GBLUP) in each panel. Broad sense heritability computed on a line means basis was low for RPR. Only 8 of 26 families had a heritability above 0.20. The NCRPIS diversity panel had a heritability of 0.54. Across NAM and IBM families, 18 family-nested QTL and 141 significant GWAS associations were identified for RPR. Numerous weak associations were also found in the NCRPIS diversity panel. However, few were linked to loci involved in phenylpropanoid and cellulose synthesis or vegetative phase transition. Using an identity-by-state (IBS) relationship matrix estimated from 1.6 million single nucleotide polymorphisms (SNPs) and RPR measures from 20% of the NAM panel, genomic prediction by GBLUP explained 64±2% of variation in the remaining RILs. In the NCRPIS diversity panel, an IBS matrix estimated from 681,257 SNPs and RPR measures from 20% of the panel explained 33±3% of variation in the remaining inbreds. These results indicate the high genetic complexity of stalk strength and the potential for genomic prediction to hasten its improvement.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The maize (Zea mays) kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications. An understanding of the regulation of kernel starch, ...protein, and oil is needed in order to manipulate composition to meet future needs. We conducted joint-linkage quantitative trait locus mapping and genome-wide association studies (GWAS) for kernel starch, protein, and oil in the maize nested association mapping population, composed of 25 recombinant inbred line families derived from diverse inbred lines. Joint-linkage mapping revealed that the genetic architecture of kernel composition traits is controlled by 21–26 quantitative trait loci. Numerous GWAS associations were detected, including several oil and starch associations in acyl-CoA:diacylglycerol acyltransferase1-2, a gene that regulates oil composition and quantity. Results from nested association mapping were verified in a 282 inbred association panel using both GWAS and candidate gene association approaches. We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content.
genetic architecture of maize height Peiffer, Jason A; Romay, Maria C; Gore, Michael A ...
Genetics (Austin),
04/2014, Letnik:
196, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pedigree or estimates of the genomic identity-by-state (IBS) among related plants, height is also ...accurately predictable. But, mapping alleles explaining natural variation in maize height remains a formidable challenge. To address this challenge, we measured the plant height, ear height, flowering time, and node counts of plants grown in >64,500 plots across 13 environments. These plots contained >7,300 inbreds representing most publically available maize inbreds in the U.S.A. as well as families of the maize Nested Association Mapping (NAM) panel. Joint-linkage mapping of quantitative trait loci (QTL), fine mapping in near isogenic lines (NILs), genome wide association studies (GWAS), and genomic best linear unbiased prediction (GBLUP) were performed. The heritability of plant height was estimated to be over 90%. Mapping of NAM family-nested QTL revealed the largest explained about 2.1 ± 0.9% of height variation. The effects of two tropical alleles at this QTL were independently validated by fine mapping. Several significant associations found by GWAS co-localized with established height loci including brassinosteroid-deficient dwarf1, dwarf plant1, and semi-dwarf2. GBLUP explained >80% of plant height variation in the observed panels and outperformed bootstrap aggregation of family-nested QTL models in evaluations of prediction accuracy. These results revealed maize height was under strong genetic control and had a highly polygenic genetic architecture. They also showed that multiple models of genetic architecture differing in polygenicity and effect sizes can plausibly explain a population’s variation in maize height, but they may vary in predictive efficacy.
Heterosis describes the superior phenotypes observed in hybrids relative to their inbred parents. Maize is a model system for studying heterosis due to the high levels of yield heterosis and ...commercial use of hybrids.
The inbred lines from an association mapping panel were crossed to a common inbred line, B73, to generate nearly 300 hybrid genotypes. Heterosis was evaluated for seventeen phenotypic traits in multiple environments. The majority of hybrids exhibit better-parent heterosis in most of the hybrids measured. Correlations between the levels of heterosis for different traits were generally weak, suggesting that the genetic basis of heterosis is trait-dependent.
The ability to predict heterosis levels using inbred phenotype or genetic distance between the parents varied for the different traits. For some traits it is possible to explain a significant proportion of the heterosis variation using linear modeling while other traits are more difficult to predict.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Teosinte, the progenitor of maize, is restricted to tropical environments in Mexico and Central America. The pre-Columbian spread of maize from its center of origin in tropical Southern Mexico to the ...higher latitudes of the Americas required postdomestication selection for adaptation to longer day lengths. Flowering time of teosinte and tropical maize is delayed under long day lengths, whereas temperate maize evolved a reduced sensitivity to photoperiod. We measured flowering time of the maize nested association and diverse association mapping panels in the field under both short and long day lengths, and of a maize-teosinte mapping population under long day lengths. Flowering time in maize is a complex trait affected by many genes and the environment. Photoperiod response is one component of flowering time involving a subset of flowering time genes whose effects are strongly influenced by day length. Genome-wide association and targeted high-resolution linkage mapping identified ZmCCT , a homologue of the rice photoperiod response regulator Ghd7, as the most important gene affecting photoperiod response in maize. Under long day lengths ZmCCT alleles from diverse teosintes are consistently expressed at higher levels and confer later flowering than temperate maize alleles. Many maize inbred lines, including some adapted to tropical regions, carry ZmCCT alleles with no sensitivity to day length. Indigenous farmers of the Americas were remarkably successful at selecting on genetic variation at key genes affecting the photoperiod response to create maize varieties adapted to vastly diverse environments despite the hindrance of the geographic axis of the Americas and the complex genetic control of flowering time.
Summary
Crop genetic diversity for climate adaptations is globally partitioned. We performed experimental evolution in maize to understand the response to selection and how plant germplasm can be ...moved across geographical zones.
Initialized with a common population of tropical origin, artificial selection on flowering time was performed for two generations at eight field sites spanning 25° latitude, a 2800 km transect. We then jointly tested all selection lineages across the original sites of selection, for the target trait and 23 other traits.
Modeling intergenerational shifts in a physiological reaction norm revealed separate components for flowering‐time plasticity. Generalized and local modes of selection altered the plasticity of each lineage, leading to a latitudinal pattern in the responses to selection that were strongly driven by photoperiod. This transformation led to widespread changes in developmental, architectural, and yield traits, expressed collectively in an environment‐dependent manner. Furthermore, selection for flowering time alone alleviated a maladaptive syndrome and improved yields for tropical maize in the temperate zone.
Our findings show how phenotypic selection can rapidly shift the flowering phenology and plasticity of maize. They also demonstrate that selecting crops to local conditions can accelerate adaptation to climate change.
Maize is a staple food for many communities with high levels of iron deficiency anemia. Enhancing the iron concentrations and iron bioavailability of maize with traditional breeding practices, ...especially after cooking and processing, could help alleviate iron deficiency in many of these regions. Previous studies on a small number of maize genotypes and maize flour products indicated that degermination (germ fraction removed with processing) could improve the iron bioavailability of maize. This study expanded upon this research by evaluating the iron bioavailability, mineral concentrations, and phytate concentrations of 52 diverse maize genotypes before (whole kernels) and after degermination. Whole and degerminated maize samples were cooked, dried, and milled to produce corn flour. Iron bioavailability was evaluated with an
digestion Caco2 cell bioassay. In 30 of the maize genotypes, bioavailable iron increased when degerminated, thus indicating a higher fractional iron uptake because the iron concentrations decreased by more than 70% after the germ fraction was removed. The remaining 22 genotypes showed no change or a decrease in iron bioavailability after degermination. These results confirm previous research showing that the germ fraction is a strong inhibitory component for many maize varieties. Phytate concentrations in maize flours were greatly reduced with degermination. However, the relationship between phytate concentrations and the iron bioavailability of processed maize flour is complex, acting as either inhibitor or promoter of iron uptake depending on the color of the maize kernels and processing method used to produce flour. Other factors in the maize endosperm fractions are likely involved in the effects of degermination on iron bioavailability, such as vitreous or floury endosperm compositions and the polyphenol content of the bran. This study demonstrates that iron nutrition from maize can be enhanced by selecting genotypes where the inhibitory effect of the bran color and endosperm fraction are relatively low, especially after processing
degermination.
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