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—Schematic of tb1 showing the location in base pairs of the markers assayed and the degree of linkage disequilibrium between markers, as measured by r 2 . The markers that associate with branch length (BRLN) are represented by solid circles and the markers that associate with female ear length (FERL) are represented by hatched circles. Shading indicates the magnitude of the linkage disequilibrium. The scatterplot shows the trait distribution for each genotypic class at marker tb1.19. The mean for each genotypic class is represented by a horizontal line. The diamonds depict the standard errors of the means.
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In plants, many major regulatory genes that control plant growth and development have been identified and characterized. Despite a detailed knowledge of the function of these genes little is known about how they contribute to the natural variation for complex traits. To determine whether major regulatory genes of maize contribute to standing variat...
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Context 1
... the 17 additional markers tested in tb1, only 1 other marker, tb1.480indel, has a raw P-value ,0.05 for association with branch length; however, this association does not survive correction for multiple testing (supplemental Table 6 at http://www.genetics.org/supplemental/). Two of the 3 markers within tb1 (tb1.19 and tb1.20), which significantly associate with branch length (Table 3), are in LD with each other as well as with 3 other markers, tb1.12, tb1.39indel, and tb1.18 (Figure 4). At the marker within tb1 that has the strongest association with branch length, tb1.19, the C allele is dominant to the G allele (40.6 6 1.4 cm for CC, 39.9 6 1.1 cm for CG, and 35.0 6 0.9 cm for GG, Figure 4). ...
Context 2
... of the 3 markers within tb1 (tb1.19 and tb1.20), which significantly associate with branch length (Table 3), are in LD with each other as well as with 3 other markers, tb1.12, tb1.39indel, and tb1.18 (Figure 4). At the marker within tb1 that has the strongest association with branch length, tb1.19, the C allele is dominant to the G allele (40.6 6 1.4 cm for CC, 39.9 6 1.1 cm for CG, and 35.0 6 0.9 cm for GG, Figure 4). A similar trend is observed at marker tb1.15 where the G allele is domi- nant to the A allele (32.6 6 1.7 cm for AA, 38.5 6 0.9 cm for AG, and 38.8 6 1.0 cm for GG) as well as at marker tb1.20 where the C allele is dominant to the G allele (39.6 6 1.4 cm for CC, 40.5 6 1.2 cm for CG, and 35.6 6 0.9 cm for GG). ...
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Citations
... Thus, higher genetic variability for kernel protein content in teosinte constitutes potential genetic resources to identify likely sites in the genome and to increase the protein content using classical and molecular breeding approaches [8,31,32]. Since maize has been domesticated from teosinte and possesses tremendous genetic variability for several economically important traits [33], hence teosinte accessions must be utilized in marker-trait association studies; however, very few studies have focused on kernel quality so far. Teosintes have twice the protein content than cultivated maize and are assumed to be a huge repository for alleles that control protein content. ...
... Based on the population structure analysis, Fukunaga et al. have also noticed parviglumis-mexicana admixtures in annual teosinte plants grown in the Balsas River valley [54]. Weber et al. conducted an association mapping to identify major regulatory genes involved in variation between teosinte and maize that were collected from the Balsas River valley and found 10 significant associations between five candidate genes for plant and inflorescence architecture [33]. Subsequently, the same research group increased the number of individuals and marker density for more traits compared to the previous study and found similar results [55]. ...
Teosinte is the closest wild ancestor of maize and is used as a valuable resource for taxonomical, evolutionary and genetic architectural studies of maize. Teosinte is also a repository of numerous diverse alleles for complex traits, including nutritional value and stress adaptation. Accessions including teosintes, maize inbred lines and coix were investigated for kernel protein and its association with DNA markers. The proposed investigation assumed that wild accessions had different genic/allelic content and consequently expression profile than modern maize because of the domestication syndrome and bottleneck effects. Total protein content in hard stony fruit case teosinte accessions were assessed from kernels with and without seed coats, while protein content from coix and maize lines was evaluated from kernels only. The accessions were also subjected to molecular profiling using 84 SSR markers, and obtained genotypic data were used for population structure and association analysis. The results emphasize that teosintes have higher protein content (18.5% to 26.29%), followed by coix (18.26%), and the least among maize lines (9% to 11%). Among teosintes, without-seed-coat samples had 3-6% higher protein content than with-seed-coat samples. When compared to other teosinte species, Z. mays subsp. mexicana accessions showed higher protein content, ranging from 18.62% to 26.29%. All evaluated accessions were divided into four subpopulations with K = 4, and seven significant (p < 0.01) marker-trait associations were seen with umc1294, umc1171, phi091, umc2182 and bnlg292 markers, which are distributed across chromosomes 4, 5, 7, 8 and 9, respectively. We have observed that the wild relatives carry protein content-enhancing alleles and can be used as productive donor parents in pre-breeding efforts to increase the protein content of maize.
... The teosinte branched 1 (tb1) locus is an example of biological pleiotropy, which impacts the number and length of internodes in lateral branches and inflorescences due to the upregulation of gene expression in maize compared to teosinte. This upregulation results from the insertion of a Hopscotch transposable element 64 kb upstream of tb1 [9][10][11][12]. Fine-mapping of tb1 confirmed this biological pleiotropy [10,13,14]. ...
Pleiotropy-when a single gene controls two or more seemingly unrelated traits-has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56-32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low.
... Association mapping targeting candidate genes has proven successful in many instances [74]. Therefore, this approach might bring new insights into carotenoid biosynthesis as the genetic pathway has already been dissected through forward and reverse genetics in many organisms. ...
... Using a diverse population and all ancestral recombination events may improve the resolution of such a study. In comparison with bi-parental cross, one of the key advantages of association mapping population is the ability to examine a large number of alleles [74]. ...
The Xishuangbanna (XIS) cucumber is an important botanical variety, accumulating high levels of β-carotene (700 μg/100 g) in the endocarp of mature fruit compared with normal green/white flesh types (25–50 μg/100 g, fresh weight). β-carotene is an essential precursor of provitamin A synthesis required for human health, thus XIS cucumber is an appealing germplasm for vitamin A breeding programs. In this review, we highlighted the molecular research progress of XIS cucumber as well as the bottlenecks undermining its utilization in genetic breeding. The XIS cucumber was first reported in 1983; thereafter, the literature on XIS cucumber was sporadic until 2012 and 2013 following QTL mapping of the Ore gene and subsequent cloning of the CsaBCH1 gene, respectively. Whereas QTL mapping studies underlying its flowering time and fruit quality related traits have been reported, fine mapping of their candidate genes remains unknown. Cucumber fruits are mainly consumed at fresh immature stage; however, XIS cucumber accumulates β-carotene at mature fruit state, thus limiting the utilization of β-carotene derived from it. In our opinion, we believe that the production and commercialization of immature orange-fleshed cucumber would gain wider acceptance among consumers. Additionally, we highlighted a comprehensive breeding strategy, precisely for enhanced β-carotene accumulation based on prior studies of XIS cucumber coupled with those from other crops. In MAS, we proposed schematic molecular backcross breeding strategy using lines possessing both ore and fft1.1 loci. This review, therefore, provides insights of XIS cucumber research and opportunities for further genetic breeding.
... The same SNP array was used to genotype an additional data set published here. The procedure used to generate these SNPs is described in Weber et al. (2007) and van Heerwaarden et al. (2010) and the genotyping platform was generated using a discovery panel of 16 teosinte and 14 maize inbred individuals (Wright et al., 2005;Weber et al., 2007). In the new data set, 828 SNPs were genotyped in 239 individuals. ...
... The same SNP array was used to genotype an additional data set published here. The procedure used to generate these SNPs is described in Weber et al. (2007) and van Heerwaarden et al. (2010) and the genotyping platform was generated using a discovery panel of 16 teosinte and 14 maize inbred individuals (Wright et al., 2005;Weber et al., 2007). In the new data set, 828 SNPs were genotyped in 239 individuals. ...
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Summary
Hybrid zones provide an excellent opportunity for studying population dynamics and whether hybrid genetic architectures are locally adaptive. The genus Zea contains many diverse wild taxa collectively called teosinte. Zea mays ssp. parviglumis , the lowland progenitor of maize ( Zea mays ssp. mays ), and its highland relative Zea mays ssp. mexicana live parapatrically and, while putative hybrids have been identified in regions of range overlap, these have never been deeply explored.
Here we use a broadly sampled SNP data set to identify and confirm 112 hybrids between Zea mays ssp. parviglumis and Zea mays ssp. mexicana , mostly clustered in three genetically and geographically distinct hybrid groups in Central Mexico.
These hybrid groups inhabit intermediate environments relative to parental taxa. We demonstrate that these individuals are true hybrids and not products of isolation by distance or ancestral to parviglumis and mexicana. This work expands on previous studies, clearly identifying hybrid zones in Zea , genetically characterizing hybrid groups, and showing what appear to be unique genetic architectures of hybridization in distinct hybrid groups.
With the potential for local adaptation, variable hybrid zone dynamics, and differential architectures of hybridization, we present these teosinte hybrids and parental taxa as a promising model system for studying hybridization and hybrid zones.
... TB1 and its homologue in eudicots-BRANCHED1 (BRC1)-have been studied extensively due to their role in regulating shoot branching and apical dominance (Doebley et al., 1997;Aguilar-Martínez et al., 2007). TB1/BRC1 of maize, rice, wheat, barley, tomato, pea, Arabidopsis, switchgrass, and cucumber have conserved roles in regulating outgrowth of lateral branches, with loss-of-function mutations increasing lateral branch number and length, while gain-of-function alleles suppress their growth (Doebley et al., 1997;Takeda et al., 2003;Aguilar-Martínez et al., 2007;Weber et al., 2007;Minakuchi et al., 2010;Martín-Trillo et al., 2011;Ramsay et al., 2011;Braun et al., 2012;Seale et al., 2017;Bennett et al., 2016;Dixon et al., 2018;Liu et al., 2018;Zwirek et al., 2019;Shen et al., 2019). A conserved role for TB1/BRC1 in controlling height and stem elongation is, however, less clear; for example, brc1 and brc1/brc2 Arabidopsis mutants are shorter than the WT, as are tomato plants with reduced expression of BRC1, potentially due to reduced apical dominance (Finlayson et al., 2010;Martín-Trillo et al., 2011;Bennett et al., 2016;Seale et al., 2017). ...
Regulation of plant height and stem elongation has contributed significantly to improvement of cereal productivity by reducing lodging and improving distribution of assimilates to the inflorescence and grain. In wheat, genetic control of height has been largely contributed by the Reduced height-1 alleles that confer GA-insensitivity - the beneficial effects of these alleles are associated with less favourable effects involving seedling emergence, grain quality and inflorescence architecture that has driven new research investigating genetic variation of stem growth. Here, we show that TEOSINTE BRANCHED1 (TB1) regulates height of wheat, with TB1 being expressed at low levels in nodes of the main culm prior to elongation, and increased dosage of TB1 restricting elongation of stem internodes. The effect of TB1 on stem growth is not partnered by poor seedling emergence, as transgenic lines with increased activity of TB1 form longer coleoptiles than null transgenic controls. Analysis of height in a multi-parent mapping population also shows that allelic variation for TB1 on the B genome influences height, with plants containing the variant TB-B1b allele being taller than those with the wild-type TB-B1a allele. Our results show that TB1 restricts height and stem elongation in wheat, suggesting variant alleles that alter the expression or function of TB1 could be used as a new source of genetic diversity for optimising architecture of wheat in breeding programs.
... For example, ZmCCT10 and ZmCCT9 were mapped and cloned using this method in a maize-teosinte BC 2 S 3 population (Hung et al., 2012;Huang et al., 2018). Association mapping in a teosinte population has also been demonstrated to be a powerful approach by which to detect significant associations between genes and traits (Weber et al., 2007(Weber et al., , 2008. However, these two studies performed candidate-gene-association analyses using <150 markers. ...
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
... The SNPs are excellent genetic markers for various genotyping applications ( Bhattramakki et al. 2002), including assessment of genetic diversity (Monna et al. 2006;Hamblin et al. 2007;Varshney et al. 2008), evolutionary studies ( Varshney et al. 2007;Caicedo et al. 2007), construction of high resolution genome maps ), detection of genome-wide linkage disequilibrium (LD, Kim et al. 2007;Mather et al. 2007) patterns and population substructure ( Schmidt et al. 2006;Caicedo et al. 2007), association mapping of genes/QTLs controlling complex traits ( Ravel et al. 2006;Li et al. 2008) and marker-assisted breeding ( Li et al. 2008;Dracatos et al. 2008;Van et al. 2008) in many plant species. A number of SNP markers in plants have been identified to be associated with genes regulating various agronomic traits such as betaine aldehyde dehydrogenase-2 gene for fragrance trait (Bradbury et al. 2005), starch synthase IIa gene for starch gelatinization temperature ( Waters et al. 2005;Bao et al. 2006), and qSH1 ( Konishi et al. 2006) and Sh4 ( Li et al. 2006) genes underlying QTLs with the seed shattering in rice, teosinte branched 1 gene for plant or inflorescence architecture in maize (Weber et al. 2007), Lr1 (Tyrka et al. 2004) and Pm3 (Tommasini et al. 2006) genes for leaf rust and powdery mildew resistance, respectively in wheat, ß-amylase gene for enzyme thermostability in barley (Paris et al. 2001;Chiapparino et al. 2003) and Dwarf8 gene for flowering time in maize ( Anderson et al. 2005). The SNP markers are useful for isolation of these economically important candidate genes harbouring QTLs through map-based cloning (Tander et al. 2002). ...
... Even though the importance of genome-wide association studies (GWAS) has increased in recent years, candidate gene association studies allow a direct identification of genes, which play a role in the performance of the pathogen population, even when the genome information is still scarce [49]. This methodology has helped in the detection of genes for important traits in different organisms, such as maize [50,51], rice [52], wheat [53], Arabidopsis [54], and humans [20]. Moreover, this approach was successfully used to study aggressiveness and mycotoxin production in Fusarium species in wheat [14,21]. ...
Fusarium culmorum
is one of the species causing Fusarium head blight (FHB) in cereals in Europe. We aimed to investigate the association between the nucleotide diversity of tenF. culmorumcandidate genes and field ratings of aggressiveness in winter rye. A total of 100F. culmorumisolates collected from natural infections were phenotyped for FHB at two locations and two years. Variance components for aggressiveness showed significant isolate and isolate-by-environment variance, as expected for quantitative host-pathogen interactions. Further analysis of the isolate-by-environment interaction revealed the dominant role of the isolate-by-year over isolate-by-location interaction. One single-nucleotide polymorphism (SNP) in the cutinase (CUT) gene was found to be significantly (p< 0.001) associated with aggressiveness and explained 16.05% of the genotypic variance of this trait in rye. The SNP was located 60 base pairs before the start codon, which suggests a role in transcriptional regulation. Compared to a previous study in winter wheat with the same nucleotide sequences, a larger variation of pathogen aggressiveness on rye was found and a different candidate gene was associated with pathogen aggressiveness. This is the first report on the association of field aggressiveness and a host-specific candidate gene codifying for a protein that belongs to the secretome inF. culmorum.
... Another potential explanation is that domestication largely acts on preexisting standing variation within a wild progenitor species and which genes were targets of artificial selection is largely determined by which alleles were segregating in the target wild population. Genes such as tb1, zfl2 ,zagl1, and zap1 all show evidence of exhibiting standing functional variation in teosinte prior to the initial domestication of maize 12,64,65 . However, it must be noted that there are indeed significant differences in the domestication process between the two species. ...
The domestication of diverse grain crops from wild grasses resulted from artificial selection for a suite of overlapping traits producing changes referred to in aggregate as ”domestication syndrome”. Parallel phenotypic change can be accomplished by either selection on orthologous genes, or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many ”classic” domestication genes identified through QTL mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that, while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization portion of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.
... Therefore, in the recent past, several other methods have been developed to accelerate the identification of function of gene/QTL underlying the trait of interest. These methods followed both forward and reverse genetic approaches including insertional mutagenesis (loss of gene function cause change in phenotype) using TDNA and transposable elements (Meissner et al. 2000;Hayes 2003;Twyman and Kohli 2003;Acosta-García et al. 2004;Tierney and Lamour 2005;Lazarow and Lütticke 2009;Chudalayandi 2011), homologous recombination mediated gene transfer (Hanin and Paszkowski 2003;Iida and Terada 2004;Tierney and Lamour 2005;Fu et al. 2012), gene silencing via RNAi (Waterhouse et al. 1998;Baulcombe 2004;Kusaba 2004;Vaucheret 2006;Eamens et al. 2008;Hebert et al. 2008;Ghildiyal and Zamore 2009;Fu et al. 2011;Mann et al. 2011;Duan et al. 2012;Ré et al. 2012;Rubinelli et al. 2013), virus induced gene silencing (Deng et al. 2012;Kachroo and Ghabrial 2012;Hosseini et al. 2012), TILLING (Ramos et al. 2009;Chen et al. 2012) and candidate gene association mapping (Wilson et al. 2004;Weber et al. 2007Weber et al. , 2008Kloosterman et al. 2010). These approaches could establish the function of genes/QTLs, which was not known previously. ...
Advancement in the field of genetics and genomics after the discovery of Mendel’s laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers’ field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
