scholarly journals Not so local: the population genetics of convergent adaptation in maize and teosinte

2021 ◽  
Author(s):  
Silas Tittes ◽  
Anne Lorant ◽  
Sean McGinty ◽  
John F. Doebley ◽  
James B. Holland ◽  
...  
Keyword(s):  
Population Genetics ◽  
Zea Mays ◽  
Local Adaptation ◽  
Genetic Architecture ◽  
Wild Relative ◽  
Selective Sweeps ◽  
Sympatric Population ◽  
Geographic Scale ◽  
Standing Variation ◽  
Maize Populations

ABSTRACTWhat is the genetic architecture of local adaptation and what is the geographic scale that it operates over? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are frequently shared by several populations, and often between the subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, post domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, out results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations, but smaller than the species range.

scholarly journals Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

2021 ◽  
Author(s):  
Erin Calfee ◽  
Daniel Gates ◽  
Anne Lorant ◽  
M. Taylor Perkins ◽  
Graham Coop ◽  
...  
Keyword(s):  
Zea Mays ◽  
Local Adaptation ◽  
Rapid Evolution ◽  
High Elevation ◽  
Chromosome 9 ◽  
Sequencing Data ◽  
Sympatric Populations ◽  
Maize Populations ◽  
Elevational Range ◽  
Local Sourcing

AbstractWhile often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays), and its wild teosinte relative. Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of Zea mays ssp. mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed >1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized Inv4m and a new 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. The bulk of our ancestry selection outliers show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize landrace populations.

scholarly journals Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

PLoS Genetics ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. e1009810
Author(s):  
Erin Calfee ◽  
Daniel Gates ◽  
Anne Lorant ◽  
M. Taylor Perkins ◽  
Graham Coop ◽  
...  
Keyword(s):  
Zea Mays ◽  
Local Adaptation ◽  
High Elevation ◽  
Chromosome 9 ◽  
Sequencing Data ◽  
Sympatric Populations ◽  
Maize Populations ◽  
Outlier Loci ◽  
Elevational Range ◽  
Local Sourcing

While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.

scholarly journals Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

2018 ◽  
Author(s):  
Markus G Stetter ◽  
Kevin Thornton ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Genetic Architecture ◽  
Genetic Basis ◽  
Stabilizing Selection ◽  
Relative Importance ◽  
Selective Sweeps ◽  
Weak Selection ◽  
Standing Variation ◽  
Polygenic Adaptation ◽  
Maize Domestication ◽  
New Mutations

ABSTRACTUnderstanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics. While technological advances now allow interrogation of genome-wide genotyping data in large panels, our understanding of the process of polygenic adaptation is still limited. To address this limitation, we use extensive forward-time simulation to explore the impacts of variation in demography, trait genetics, and selection on the rate and mode of adaptation and the resulting genetic architecture. We simulate a population adapting to an optimum shift, modeling sequence variation for 20 QTL for each of 12 different demographies for 100 different traits varying in the effect size distribution of new mutations, the strength of stabilizing selection, and the contribution of the genomic background. We then use random forest regression approaches to learn the relative importance of input parameters in determining a number of aspects of the process of adaptation including the speed of adaptation, the relative frequency of hard sweeps and sweeps from standing variation, or the final genetic architecture of the trait. We find that selective sweeps occur even for traits under relatively weak selection and where the genetic background explains most of the variation. Though most sweeps occur from variation segregating in the ancestral population, new mutations can be important for traits under strong stabilizing selection that undergo a large optimum shift. We also show that population bottlenecks and expansion impact overall genetic variation as well as the relative importance of sweeps from standing variation and the speed with which adaptation can occur. We then compare our results to two traits under selection during maize domestication, showing that our simulations qualitatively recapitulate differences between them. Overall, our results underscore the complex population genetics of individual loci in even relatively simple quantitative trait models, but provide a glimpse into the factors that drive this complexity and the potential of these approaches for understanding polygenic adaptation.Author summaryMany traits are controlled by a large number of genes, and environmental changes can lead to shifts in trait optima. How populations adapt to these shifts depends on a number of parameters including the genetic basis of the trait as well as population demography. We simulate a number of trait architectures and population histories to study the genetics of adaptation to distant trait optima. We find that selective sweeps occur even in traits under relatively weak selection and our machine learning analyses find that demography and the effect sizes of mutations have the largest influence on genetic variation after adaptation. Maize domestication is a well suited model for trait adaptation accompanied by demographic changes. We show how two example traits under a maize specific demography adapt to a distant optimum and demonstrate that polygenic adaptation is a well suited model for crop domestication even for traits with major effect loci.

scholarly journals Combining Ability and Heterosis of Algerian Saharan Maize Populations (Zea mays L.) for Tolerance to No-Nitrogen Fertilization and Drought

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 492
Author(s):  
Meriem Riache ◽  
Pedro Revilla ◽  
Oula Maafi ◽  
Rosa Ana Malvar ◽  
Abderahmane Djemel
Keyword(s):  
Zea Mays ◽  
Stress Tolerance ◽  
Nitrogen Fertilization ◽  
Recurrent Selection ◽  
Zea Mays L ◽  
Base Material ◽  
N Fertilization ◽  
Nitrogen Stress ◽  
Reciprocal Recurrent Selection ◽  
Maize Populations

Drought and low nitrogen are major stresses for maize (Zea mays L.), and maize populations from the Sahara Desert are potential sources of stress tolerance. The objectives were to assess the tolerance and varietal and heterosis effects of Algerian populations under no-nitrogen fertilization and water stress. A diallel among six Algerian maize population was evaluated under drought (300 mm irrigation) vs. control (600 mm) and no-nitrogen fertilization vs. 120 kh ha−1 N fertilization. Genotypes showed significant differences and genetic effects for water- and nitrogen-stress tolerance. We propose a reciprocal recurrent selection to take advantage of additive and non-additive effects, using AOR and IGS, since they showed good performance in optimum and stress conditions, for improving yield heterosis for AOR × IGS. Negative effects are not expected on plant height, anthesis–silking interval or early vigor. These populations and BAH could be sources of inbred lines tolerant to drought and no-nitrogen fertilization. There was no relationship between origin and genetic group and stress tolerance per se or as parents of tolerant crosses. These populations and crosses could be used as base material among Algerian populations, for breeding programs focusing on tolerance to water or nitrogen stress.

scholarly journals SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

2022 ◽  
Author(s):  
Tiago da Silva Ribeiro ◽  
José A Galván ◽  
John E Pool
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Genetic Variant ◽  
Real Data ◽  
Selective Sweeps ◽  
Functional Categories ◽  
Genome Scans ◽  
Genome Wide ◽  
A Genome ◽  
Local Selection

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

scholarly journals The Genetic Architecture of Maize (Zea mays L.) Kernel Weight Determination

2014 ◽  
Vol 4 (9) ◽  
pp. 1611-1621 ◽  
Author(s):  
S. Alvarez Prado ◽  
C. G. Lopez ◽  
M. L. Senior ◽  
L. Borras
Keyword(s):  
Zea Mays ◽  
Genetic Architecture ◽  
Zea Mays L ◽  
Kernel Weight

scholarly journals Inter- and intra-population variation of local maize (Zea mays L.) populations from Slovakia and Czech Republic

2008 ◽  
Vol 43 (No. 1) ◽  
pp. 7-15 ◽  
Author(s):  
P. Múdry ◽  
J. Kraic
Keyword(s):  
Zea Mays ◽  
Genetic Variation ◽  
Czech Republic ◽  
Population Variation ◽  
Polymorphic Loci ◽  
Maize Populations ◽  
Expected Heterozygosity ◽  
Isoenzyme Polymorphism ◽  
New Alleles

Evaluation of genetic variation was performed within 62 local maize populations originating from Slovakia and Czech Republic. In total 48 alleles at 22 analyzed isoenzyme loci with an average of 2.2 alleles per locus were revealed. The percentage of polymorphic loci ranged from 14% to 59% and the frequencies of detected alleles varied from null to four per locus. No polymorphism was detected at the loci <i>Dia2</i>, <i>Got3</i>, <i>Mdh4</i>, <i>Mmm</i>, and <i>Pgm1</i>. The highest number of alleles (four) was detected at loci <i>Acp1</i>, <i>Cat3</i>, <i>Pgm2</i>. No new alleles were identified, nevertheless the frequency of seven alleles was only about 1%. The expected heterozygosity ranged from null to 0.492 with an average of 0.197. The revealed isoenzyme polymorphism confirmed that all analyzed populations were heterogeneous and as many as 17 of them were completely heterogeneous. None of the analyzed populations was identical in the frequency of alleles at all 22 analyzed loci.

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