Biology subjects

Lorant, A.

Publications and source records attributed to Lorant, A..

8 recordsLinked to original sources

bioRxiv2025

HERITABILITY AND QTL MAPPING OF AERIAL ROOTS AND OTHER YIELD COMPONENT TRAITS WITH IMPLICATIONS FOR N2 FIXATION IN ZEA MAYS

Zea mays L. spp. mays (hereafter maize) populations from an indigenous community of Mexico have been reported to perform well using traditional cultivation practices that exclude industrial fertilizers despite low soil nitrate levels. The local maize cultivar is characterized by extended maturity, tall stature, and presence of thick aerial roots that secrete an abundance of polysaccharide-rich root exudate, or mucilage, that is implicated in the recruitment of diazotrophic microbes to facilitate biological nitrogen fixation. Here we estimate the broad sense heritability of traits related to nitrogen fixation in a panel of Zea entries spanning pre-domestication, post-domestication and post-improvement, and identify QTL via F2:F3 families for traits including aerial root node counts and various other yield related traits (i.e. germination rate, time to reproductive maturity, total biomass and nitrogen content of shoot and grain). Across two separate field studies, aerial root node count (AR) demonstrates heritability of 64% and 73%, and genetic mapping reveals three distinct QTL distributed on chromosomes 1 and 9. Further, we report novel QTL for germination rate via stand counts after direct sowing (SC), Plant Total Nitrogen (PTN), Plant Dry Mass (PDM), and a joint QTL for Grain Total Nitrogen (GTN) and Grain Dry Mass (GDM). Finally, we identify overlap between QTL for multiple traits (including AR and SC) and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana) into Totontepec maize, with a greater degree of overlap than expected under a uniform genomic distribution suggesting adaptive introgression from mexicana. Given its pronounced aerial root morphology, we propose that mexicana is the ancestral source for prominent aerial roots and corresponding abundant mucilage production in Totontepec maize and other maize traditional varieties. ARTICLE SUMMARYZea mays aerial roots (AR) and mucilage have been implicated in diazotrophic recruitment. This study estimates heritability and identifies QTL for AR and yield components via a diverse panel of Zea entries and F2:F3 mapping populations. Genetic mapping reveals three QTL for AR and several QTL for other yield traits, both novel and previously reported. This study also compares QTL and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana) into a native cultivar. For AR QTL, enrichment for mexicana-derived haplotypes is greater than expected under a uniform genomic distribution, suggesting adaptive introgression from mexicana.

genetics↗

bioRxiv2021

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

What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? 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 also frequently shared by several populations, and often between 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, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our 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.

evolutionary biology↗

bioRxiv2021

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

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 maizes 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 FSTbetween 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. Author SummaryWhen species expand their ranges, new encounters with diverse wild relatives can introduce deleterious genetic variation, but may also accelerate the colonization of novel environments by providing ready-made genetic adaptations. Maize today is a global staple, far exceeding the original ecological niche of its wild progenitor. We show that gene flow from highland-endemic wild mexicana facilitated maizes range expansion from the valleys where it was domesticated to sites over 1500m in the mountains of Mexico. We find loci where mexicana ancestry has been repeatedly favored in highland maize populations. We also find loci (including a newly identified inversion) where mexicana ancestry increases steeply with elevation, providing evidence for adaptive trade-offs. We additionally demonstrate selection against mexicana ancestry, especially near domestication genes. We sampled mexicana growing alongside maize fields, yet find little evidence that introgression is recent or locally-sourced genomewide or at adaptive loci. Rather, the majority of mexicana ancestry was introduced into maize over 1000 generations ago, and subsequently diverged and was sorted by selection in individual populations. These results add to our understanding of the effects of introgression on range expansions and adaptation.

evolutionary biology↗

bioRxiv2020

Male linked genomic regions determine sex in dioecious Amaranthus palmeri

Dioecy, the separation of reproductive organs on different individuals, has evolved repeatedly in different plant families. Several evolutionary paths to dioecy have been suggested, but the mechanisms behind sex determination is not well understood. The diploid dioecious Amaranthus palmeri represents a well suited model system to study sex determination in plants. A. palmeri is one of the most troublesome weeds in the US, has successfully colonized other regions in the world and has evolved resistance to several herbicide classes. Despite the agricultural importance of the species, the genetic control and evolutionary state of dioecy in A. palmeri is currently unknown. Early cytogenetic experiments did not identify heteromorphic chromosomes. Here, we used whole genome sequencing of male and female pools from two independent populations to elucidate the genetic control of dioecy in A. palmeri. Read alignment to a close monoecious relative and allele frequency comparisons between male and female pools did not reveal significant sex linked genes. Consequently, we employed an alignment free k-mer comparison which enabled us to identify a large number of male specific k-mers. We assembled male specific contigs comprising a total of almost 2 Mb sequence, proposing a XY sex determination system in the species. Based on our findings we suggest an intermediate evolutionary state of dioecy in A. palmeri. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.

plant biology↗

bioRxiv2019

Chromosome Evolution of Octoploid Strawberry

The allo-octoploid cultivated strawberry (Fragaria x ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. x ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information, and unifying existing chromosome nomenclatures. Through comparative genetic mapping, we show that the genomes of geographically diverse wild octoploids are effectively diploidized and completely collinear. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported both its origin and domestication through repeated cycles of interspecific hybridization.

genomics↗

bioRxiv2017

Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.\n\nAuthor summaryGenome size in plants can vary by orders of magnitude, but this variation has long been considered to be of little to no functional consequence. Studying three independent adaptations to high altitude in Zea mays, we find that genome size experiences parallel pressures from natural selection, causing a linear reduction in genome size with increasing altitude. Though reductions in repetitive content are responsible for the genome size change, we find that only those individual loci contributing most to the variation in genome size are individually targeted by selection. To identify the phenotype influenced by genome size, we study how variation in genome size within a single teosinte population impacts leaf growth and cell division. We find that genome size variation correlates negatively with the rate of cell division, suggesting that individuals with larger genomes require longer to complete a mitotic cycle. Finally, we reanalyze data from maize inbreds to show that faster cell division is correlated with earlier flowering, connecting observed variation in genome size to an important adaptive phenotype.

evolutionary biology↗

bioRxiv2017

The interplay of demography and selection during maize domestication and expansion

The history of maize has been characterized by major demographic events including changes in population size associated with domestication and range expansion as well as gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes. Here, we investigate these processes based on high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize as well as four wild progenitor individuals (Zea mays ssp. parviglumis) from the Balsas River Valley in Mexico. Genome-wide demographic analyses reveal that maize domestication and spread resulted in pronounced declines in effective population size due to both a protracted bottleneck and serial founder effects, while, concurrently, parviglumis experienced population growth. The cost of maize domestication and spread was an increase in deleterious alleles in the domesticate relative to its wild progenitor. This cost is particularly pronounced in Andean maize, which appears to have experienced a more dramatic founder event when compared to other maize populations. Introgression from the wild teosinte Zea mays ssp. mexicana into maize in the highlands of Mexico and Guatemala is found found to decrease the prevalence of deleterious alleles, likely due to the higher long-term effective population size of wild maize. These findings underscore the strong interaction between historical demography and the efficiency of selection species- and genome-wide and suggest domesticated species with well-characterized histories may be particularly useful for understanding this interplay.

evolutionary biology↗

bioRxiv2017

The Potential Role of Genetic Assimilation during Maize Domestication

Domestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. Recent research, in which maize and teosinte (i.e., wild maize) were exposed to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte and little response to environment in maize. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial re-wiring of expression networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.

genomics↗