Wild Relatives Of Maize Research Articles

Creation of doubled haploid lines of maize <i>Zea mays</i> L. by resynthesis from a tetraploid population

The search for new, effective methods for broadening the genetic polymorphism of the original breeding material remains one of important problems of hybrid maize breeding. Globally, breeding of commercial maize varieties and hybrids is carried out using diploid genotypes, whereas tetraploid sources of initial material and wild relatives of maize are poorly involved in the breeding process. The direct heteroploid crosses between diploid and tetraploid genotypes lead to the formation of weakly fertile or completely sterile triploid hybrids, which are cytologically unstable in subsequent generations. Tetraploid maize (2n=40), as well as some wild relatives with tetraploid genome, such as Zea perennis Hitchk. (2n=40) and Tripsacum dactiloides (L.) L. (2n=72), are attractive to breeders as sources for improving economically valuable traits. The attractiveness of resynthesized diploid lines is explained by the fact that unequal crossing over between homologous chromosomes forming polyvalent associations of chromosomes, more chromosomal rearrangements occur in tetraploids than in diploid genotypes, the chromosomes of which form bivalents. Synthetic tetraploid populations of maize and its tetraploid wild relatives have great potential of variability for improving diploid maize. The authors proposed a direct method for the resynthesis of doubled haploid lines using haploid induction and an indirect method for obtaining diploid lines by heteroploid crossing and subsequent segregation of a triploid hybrid in the progeny. The method of resynthesizing the tetraploid maize genome to diploid serves as an ideal model for studying the processes of crossing over in meiosis between multivalent associations of homologous chromosomes; it is promising for obtaining diploid lines with an increased frequency of recombination between the homologous chromosomes of different genomes, combined into a common one, and can serve as a source for obtaining aneuploid series.

QTL-seq and transcriptomic integrative analyses reveal two positively regulated genes that control the low-temperature germination ability of MTP–maize introgression lines

Two candidate genes (ZmbZIP113 and ZmTSAH1) controlling low-temperature germination ability were identified by QTL-seq and integrative transcriptomic analyses. The functional verification results showed that two candidate genes positively regulated the low-temperature germination ability of IB030. Low-temperature conditions cause slow maize (Zea mays L.) seed metabolism, resulting in slow seedling emergence and irregular seedling emergence, which can cause serious yield loss. Thus, improving a maize cultivar's low-temperature germination ability (LTGA) is vital for increasing yield production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant of cold stress and can thus be used to improve the LTGA of maize. In a previous study, the genetic bridge MTP was constructed (from maize, T. dactyloides, and Z. perennis) and used to obtain a highly LTGA maize introgression line (IB030) by backcross breeding. In this study, IB030 (Strong-LTGA) and Mo17 (Weak-LTGA) were selected as parents to construct an F2 offspring. Additionally, two major QTLs (qCS1-1 and qCS10-1) were mapped. Then, RNA-seq was performed using seeds of IB030 and the recurrent parent B73 treated at 10°C for 27 days and 25°C for 7 days, respectively, and two candidate genes (ZmbZIP113 and ZmTSAH1) controlling LTGA were located using QTL-seq and integrative transcriptomic analyses. The functional verification results showed that the two candidate genes positively regulated LTGA of IB030. Notably, homologous cloning showed that the source of variation in both candidate genes was the stable inheritance of introgressed alleles from Z. perennis. This study was thus able to analyze the LTGA mechanism of IB030 and identify resistance genes for genetic improvement in maize, and it proved that using MTP genetic bridge confers desirable traits or phenotypes of Z. perennis and tripsacum essential to maize breeding systems.

QTL Mapping and a Transcriptome Integrative Analysis Uncover the Candidate Genes That Control the Cold Tolerance of Maize Introgression Lines at the Seedling Stage.

Chilling injury owing to low temperatures severely affects the growth and development of maize (Zea mays.L) seedlings during the early and late spring seasons. The existing maize germplasm is deficient in the resources required to improve maize's ability to tolerate cold injury. Therefore, it is crucial to introduce and identify excellent gene/QTLs that confer cold tolerance to maize for sustainable crop production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant to cold and can be used to improve the cold tolerance of maize. In a previous study, a genetic bridge among maize that utilized Z. perennis and T. dactyloides was created and used to obtain a highly cold-tolerant maize introgression line (MIL)-IB030 by backcross breeding. In this study, two candidate genes that control relative electrical conductivity were located on MIL-IB030 by forward genetics combined with a weighted gene co-expression network analysis. The results of the phenotypic, genotypic, gene expression, and functional verification suggest that two candidate genes positively regulate cold tolerance in MIL-IB030 and could be used to improve the cold tolerance of cultivated maize. This study provides a workable route to introduce and mine excellent genes/QTLs to improve the cold tolerance of maize and also lays a theoretical and practical foundation to improve cultivated maize against low-temperature stress.

Genome sequencing reveals evidence of adaptive variation in the genus Zea.

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

Advances in research and utilization of maize wild relatives

<p indent="0mm">Maize (<italic>Zea mays</italic> ssp. <italic>mays</italic>, 2<italic>n</italic>=2<italic>x</italic>=20), which belongs to the <italic>Zea</italic> genera of the Maydeae tribe of the Gramineae family, is an important crop in guaranteeing national food security due to its high grain yield, forage yield and nutritive value for human food and animal feed as well as its use as an industrial material. The development and application of hybrid breeding, generous use of pesticides and fertilizers, and continuous improvement of cultivation techniques have greatly improved the yield of maize in the past several decades. However, this growth in yield has been declining. Meanwhile, the occurrence of recent extreme weather events threatens maize production. In addition, due to prevailing crop breeding practices, yield-related traits have been focused on by plant breeders, which led to narrowing genetic diversity of maize germplasm, severe cultivar homogeneity, and poor resistance to biotic and abiotic stress. Therefore, it is of the utmost importance to cultivate newer maize varieties that are highly adaptable to unfavorable environments, along with high yielding and excellent quality. Crop wild relatives (CWRs) appear promising in enhancing the genetic diversity of cultivated crops. The wild relatives of maize, such as teosinte and <italic>Tripsacum</italic> L., contain abundant genetic variation and excellent resistance to salt, cold, disease, and insect. They are a treasure for maize breeding and mining excellent exogenous gene resources. In this review, we will first discuss the phylogeny and cross-compatibility of maize and its wild relatives. Although previous studies have investigated the phylogeny and cross-compatibility of maize, teosinte and <italic>Tripsacum</italic> L. in detail, the phylogeny and cross-compatibility of maize and its wild relatives have recently been further clarified based on phenotypic, molecular geographic, and genomic evidence. Secondly, we will describe the advances in genomics of maize and its wild relatives. Over the past decade, reference genome or transcriptome sequences have been obtained for numerous crops. However, genomic studies of CWRs have trailed behind those of domesticated and other model plants. The opportunities afforded by CWRs reference genomes are only now beginning to be realized thanks to diminishing cost of next-generation sequencing technologies making population-scale data feasible. Thirdly, we will systematically cover the recent successful utilization of maize wild relatives in maize breeding for improvements in yield and quality, biotic and abiotic stress resistance, perennial maize, and forage maize. These success examples demonstrate that maize wild relatives are effective and valuable to feed back into the improvement of maize. Lastly, we will discuss the future development and research direction of maize wild relatives. It is urgent to strengthen the collection, protection and genome sequencing of maize wild relatives, and establish maize-teosinte mapping populations, including classic F₂, backcross, chromosome segment substitution line, and recombinant inbred line (RIL). Molecular markers based on the genome and transcriptome of maize and its wild relatives will be utilized to construct linkage maps and to map QTLs or genes. The cross between maize and <italic>Tripsacum</italic> is extremely difficult under the natural state, but the polyploid as bridge material (such as MTP, a maize-<italic>T</italic>.<italic> dactyloides</italic>-<italic>Z</italic>.<italic> perennis</italic> allohexaploid) can transfer <italic>T</italic>.<italic> dactyloides</italic> genes introgressed into maize. <italic>De novo</italic> domestication of maize wild relatives via gene editing technology, functional genomics and bioinformatics will accelerate maize improvement. This review aims to provide important insights into how maize wild relatives can be utilized as a powerful gene pool for improving maize varieties and guaranteeing national food security.

Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize.

Climate change is one of the most important threats to biodiversity and crop sustainability. The impact of climate change is often evaluated on the basis of expected changes in species' geographical distributions. Genomic diversity, local adaptation, and migration are seldom integrated into future species projections. Here, we examine how climate change will impact populations of two wild relatives of maize, the teosintes Zea mays ssp. mexicana and Z. mays ssp. parviglumis. Despite high levels of genetic diversity within populations and widespread future habitat suitability, we predict that climate change will alter patterns of local adaptation and decrease migration probabilities in more than two-thirds of present-day teosinte populations. These alterations are geographically heterogeneous and suggest that the possible impacts of climate change will vary considerably among populations. The population-specific effects of climate change are also evident in maize landraces, suggesting that climate change may result in maize landraces becoming maladapted to the climates in which they are currently cultivated. The predicted alterations to habitat distribution, migration potential, and patterns of local adaptation in wild and cultivated maize raise a red flag for the future of populations. The heterogeneous nature of predicted populations' responses underscores that the selective impact of climate change may vary among populations and that this is affected by different processes, including past adaptation.

Wild Relatives of Maize, Rice, Cotton, and Soybean: Treasure Troves for Tolerance to Biotic and Abiotic Stresses.

Global food demand is expected to nearly double by 2050 due to an increase in the world's population. The Green Revolution has played a key role in the past century by increasing agricultural productivity worldwide, however, limited availability and continued depletion of natural resources such as arable land and water will continue to pose a serious challenge for global food security in the coming decades. High yielding varieties with proven tolerance to biotic and abiotic stresses, superior nutritional profiles, and the ability to adapt to the changing environment are needed for continued agricultural sustainability. The narrow genetic base of modern cultivars is becoming a major bottleneck for crop improvement efforts and, therefore, the use of crop wild relatives (CWRs) is a promising approach to enhance genetic diversity of cultivated crops. This article provides a review of the efforts to date on the exploration of CWRs as a source of tolerance to multiple biotic and abiotic stresses in four global crops of importance; maize, rice, cotton, and soybean. In addition to the overview of the repertoire and geographical spread of CWRs in each of the respective crops, we have provided a comprehensive discussion on the morphological and/or genetic basis of the traits along with some examples, when available, of the research in the transfer of traits from CWRs to cultivated varieties. The emergence of modern molecular and genomic technologies has not only accelerated the pace of dissecting the genetics underlying the traits found in CWRs, but also enabled rapid and efficient trait transfer and genome manipulation. The potential and promise of these technologies has also been highlighted in this review.

Connecting genomic patterns of local adaptation and niche suitability in teosintes.

The central abundance hypothesis predicts that local adaptation is a function of the distance to the centre of a species' geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals of adaptation. We identified candidate adaptive SNPs in each population by combining neutrality tests and cline analyses. By applying linear regression models, we found that the number of candidate SNPs is positively associated with niche suitability, while genetic diversity is reduced at the limits of the geographic distribution. Our results suggest that overall, populations located at the limit of the species' niches are adapting locally. We argue that local adaptation to this limit could initiate ecological speciation processes and facilitate adaptation to global change.

Modulation of AUXIN-BINDING PROTEIN 1 gene expression in maize and the teosintes by transposon insertions in its promoter

Auxin plays crucial roles in plant development. Auxin-binding protein 1 (ABP1) is an auxin receptor required to coordinate cell division and expansion during postembryonic shoot development, and differential auxin responses during root growth. While ABP1 is encoded by a single gene in maize, multiple gene copies exist in teosinte, the wild relatives of maize. We have previously shown that some of the differences between these genes are caused by multiple transposon insertions in the promoter. Here we show that the different ABP1 promoter types confer differential gene expression levels on a firefly luciferase reporter gene. We also discovered a negative regulatory sequence upstream of the conserved transcriptional start site. When this sequence is insulated by an Ac-like transposon or deleted in natural ABP1 gene variants, expression levels are enhanced. Promoters combining both a MITE and a solo-LTR showed small but significant increase in expression compared to those containing only one insertion. This increase seems to be additive, suggesting that it may be due to enhancer sequences present within these transposons. Our results point to a potential role of the ABP1-associated transposons in the modulation of ABP1 gene expression.

Single-Gene Detection and Karyotyping Using Small-Target Fluorescence in Situ Hybridization on Maize Somatic Chromosomes

Combined with a system for identifying each of the chromosomes in a genome, visualizing the location of individual genetic loci by fluorescence in situ hybridization (FISH) would aid in assembling physical and genetic maps. Previously, large genomic clones have been successfully used as FISH probes onto somatic chromosomes but this approach is complicated in species with abundant repetitive elements. In this study, repeat-free portions of sequences that were anchored to particular chromosomes including genes, gene clusters, large cDNAs, and portions of BACs obtained from public databases were used to label the corresponding physical location using FISH. A collection of probes that includes at least one marker on each chromosome in the maize complement was assembled, allowing a small-target karyotyping system to be developed. This set provides the foundation onto which additional loci could be added to strengthen further the ability to perform chromosomal identification in maize and its relatives. The probes were demonstrated to produce signals in several wild relatives of maize, including Zea luxurians, Z. diploperennis, and Tripsacum dactyloides.

Differentiation of the American and Oriental Maydeae Accessions Using the Maize Simple Sequence Repeat (SSR) Markers

The present study evaluated the utility of maize microsatellite markers in genotype differentiation and analysis of genetic diversity among the Oriental Maydeae accessions (Coix aquatica and Chionachne koenigii) vis-a-vis the American Maydeae (maize, teosintes and maize-teosinte derivatives). Analysis of 27 microsatellite loci distributed throughout the maize genome led to the detection of 89 SSR alleles at average of 3.30 per locus. Polymorphism information content (PIC) values and observed genetic distances showed the existence of large variability among the various accessions. The maize SSR markers, particularly nc013, phi059, bnlg1523 and umc1014, were highly effective in differentiating the Oriental Maydeae accessions from the American Maydeae. Cluster analysis and Principal Component Analysis based on the SSR data clearly indicated significant genetic divergence between the Oriental Maydeae and the American Maydeae accessions, as well as between Coix aquatica and Chionachne koenigii. Molecular analyses would be valuable in gaining a better understanding of genera belonging to the Oriental Maydeae, the lesser known wild relatives of maize.

Conservation and Change: A Comparison of In situ and Ex situ Conservation of Jala Maize Germplasm

Conservation of agricultural genetic resources, whether in situ (in farmers' fields) or ex situ (in a germplasm repository), provides variation for breeding and selection efforts. In this study, we assayed levels of genetic diversity from in situ and ex situ populations of Jala, a very tall, large‐eared race of maize (Zea mays L. subsp. mays), using 22 simple sequence repeat (SSR) loci. For comparison, we also analyzed diversity in reference populations of other maize races and wild relatives of maize, the teosintes (both Zea spp. and Z. mays subsp.). As expected, both the in situ and ex situ Jala populations were not as diverse as the teosintes (gene diversity, He, ≈ 0.60 and 0.7, respectively), but they were surprisingly more diverse than the populations representing other maize races (He = 0.55). The older ex situ Jala populations were less diverse and more differentiated than more recently collected accessions. Despite this fact, we observed similar levels of overall genetic diversity in the ex situ and in situ populations (He = 0.62 and 0.61, respectively), and little differentiation between these groups (Fst = 0.01). Therefore, the ex situ Jala collections, as a whole, contained the diversity found today in the field, even though diversity was under‐represented in individual repository populations.

Quantitative trait loci controlling phenotypes related to the perennial versus annual habit in wild relatives of maize.

We used quantitative trait locus/loci (QTL) mapping to study the inheritance of traits associated with perennialism in a cross between an annual (Zea mays ssp. parviglumis) and a perennial (Z. diploperennis) species of teosinte. The most striking difference between these species is that Z. diploperennis forms rhizomes, whereas Z. mays ssp. parviglumis lacks these over-wintering underground stems. An F2 population of 425 individuals was genotyped at 95 restriction fragment length polymorphism marker loci and the association between phenotype and genotype was analyzed by composite interval mapping. We detected a total of 38 QTL for eight traits. The number of QTL found for each trait ranged from two for rhizome formation to nine for tillering. QTL for six of the traits mapped near each other on chromosome 2, and QTL for four traits mapped near each other on chromosome 6, suggesting that these regions play an important role in the evolution of the perennial habit in teosinte. Most of the 38 QTL had small effects, and no single QTL showed a strikingly large effect. The map positions that we determined for rhizome formation and other traits in teosinte may help to locate corresponding QTL in pasture and turf grasses used as forage for cattle and for erosion control in agro-ecosystems.

Protein Distribution Pattern in Floury and Vitreous Endosperm of Maize Grain

ABSTRACTAlpha‐amino nitrogen compounds of floury and vitreous parts of hand‐dissected endosperm from eight maize (Zea mays L.) inbred lines, representing a broad range of vitreousness (42–95%), were isolated as nonprotein nitrogen, albumin‐globulins, zeins, and true glutelins. The three protein classes averaged, respectively, 13, 48, and 35% of total nitrogen in floury endosperm, and 4, 79, and 15% of that in vitreous endosperm. For six inbreds, floury endosperm was richer in 27 kDa γ‐zein than vitreous endosperm; the reverse was found for an Argentine flint inbred (ARGL 256), and only traces of 27 kDa γ‐zein occurred in both floury and vitreous endosperm of inbred F113. Results were compared with protein distribution patterns reported in the literature of whole endosperm of wild‐type and mutant genotypes of maize, and with wild relatives of maize, Tripsacum, and teosintes. When percentage of salt‐soluble nitrogen increased from 2% (Tripsacum) to 22% (in double mutant Oh43o2;bt2), zeins decreased from 87 to 22%, and true glutelins increased from 11 to 57%. The pattern of whole endosperm of Zea perennis was very similar to that of the vitreous endosperm of line ARGL 256. The mean pattern for whole endosperm of six o2 inbred lines was identical to that of floury endosperm of eight wild‐type lines, consistent with a lack of synthesis of α‐zeins due to the mutation in the O2 gene.

Gibberella fujikuroi mating population E is associated with maize and teosinte

Summary Isolates of Fusarium subglutinans mating population E are usually found on maize. This fungus forms part of the so-called Gibberella fujikuroi species complex. Previously, F. subglutinans has been associated with two additional mating populations (B and H) and a variety of plant hosts. This was mainly due to a lack of diagnostic morphological characters, but the use of DNA sequence information showed that the strains making up mating populations B, E and H, as well as those associated with the different plant hosts, represent separate species. Recently, another putative mating population has been reported on the wild teosinte relatives of maize. Based on sexual compatibility studies, these isolates were apparently closely related to the pitch canker fungus, F. subglutinans f. sp. pini (= F. circinatum;G. fujikuroi mating population H). The aim of the current study was to determine whether the population of F. subglutinans from teosinte constitutes a new or an existing lineage within the G. fujikuroi complex. For this purpose, portions of the mitochondrial small subunit ribosomal DNA, calmodulin and beta-tubulin genes from the fungi were sequenced. Phylogenetic analyses and comparison with sequences from public domain databases indicated that the F. subglutinans isolates from teosinte are most closely related to strains of G. fujikuroi mating population E. These results were confirmed using sexual compatibility studies. The putative mating population from the wild relatives of maize therefore forms part of the existing E-mating population and does not constitute a new lineage in the G. fujikuroi species complex.

Maize as a model for the evolution of plant nuclear genomes.

The maize genome is replete with chromosomal duplications and repetitive DNA. The duplications resulted from an ancient polyploid event that occurred over 11 million years ago. Based on DNA sequence data, the polyploid event occurred after the divergence between sorghum and maize, and hence the polyploid event explains some of the difference in DNA content between these two species. Genomic rearrangement and diploidization followed the polyploid event. Most of the repetitive DNA in the maize genome is retrotransposable elements, and they comprise 50% of the genome. Retrotransposon multiplication has been relatively recent-within the last 5-6 million years-suggesting that the proliferation of retrotransposons has also contributed to differences in DNA content between sorghum and maize. There are still unanswered questions about repetitive DNA, including the distribution of repetitive DNA throughout the genome, the relative impacts of retrotransposons and chromosomal duplication in plant genome evolution, and the hypothesized correlation of duplication events with transposition. Population genetic processes also affect the evolution of genomes. We discuss how centromeric genes should, in theory, contain less genetic diversity than noncentromeric genes. In addition, studies of diversity in the wild relatives of maize indicate that different genes have different histories and also show that domestication and intensive breeding have had heterogeneous effects on genetic diversity across genes.