Quantification of the effects of VRN1 and Ppd-D1 to predict spring wheat (Triticum aestivum) heading time across diverse environments.
ABSTRACT: Heading time is a major determinant of the adaptation of wheat to different environments, and is critical in minimizing risks of frost, heat, and drought on reproductive development. Given that major developmental genes are known in wheat, a process-based model, APSIM, was modified to incorporate gene effects into estimation of heading time, while minimizing degradation in the predictive capability of the model. Model parameters describing environment responses were replaced with functions of the number of winter and photoperiod (PPD)-sensitive alleles at the three VRN1 loci and the Ppd-D1 locus, respectively. Two years of vernalization and PPD trials of 210 lines (spring wheats) at a single location were used to estimate the effects of the VRN1 and Ppd-D1 alleles, with validation against 190 trials (~4400 observations) across the Australian wheatbelt. Compared with spring genotypes, winter genotypes for Vrn-A1 (i.e. with two winter alleles) had a delay of 76.8 degree days (°Cd) in time to heading, which was double the effect of the Vrn-B1 or Vrn-D1 winter genotypes. Of the three VRN1 loci, winter alleles at Vrn-B1 had the strongest interaction with PPD, delaying heading time by 99.0 °Cd under long days. The gene-based model had root mean square error of 3.2 and 4.3 d for calibration and validation datasets, respectively. Virtual genotypes were created to examine heading time in comparison with frost and heat events and showed that new longer-season varieties could be heading later (with potential increased yield) when sown early in season. This gene-based model allows breeders to consider how to target gene combinations to current and future production environments using parameters determined from a small set of phenotyping treatments.
Project description:In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross between two early flowering winter wheat cultivars. When the population was grown in the greenhouse after partial vernalization treatment, major heading date QTLs co-located with the VRN-A1 and VRN-B1 loci. Copy number variation at the VRN-A1 locus influenced HD such that RIL having three copies required longer cold exposure to transition to flowering than RIL having two VRN-A1 copies. Sequencing vrn-B1 winter alleles of the parents revealed multiple polymorphisms in the first intron that were the basis of mapping a major HD QTL coinciding with VRN-B1. A 36 bp deletion in the first intron of VRN-B1 was associated with earlier HD after partial vernalization in lines having either two or three haploid copies of VRN-A1. The VRN1 loci interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The PPD1 loci were significant determinants of heading date in the fully vernalized treatment in the greenhouse and in all field environments. Heading date QTL were associated with alleles having large deletions in the upstream regions of PPD-A1 and PPD-D1 and with copy number variants at the PPD-B1 locus. The PPD-D1 locus was determined to have the largest genetic effect, followed by PPD-A1 and PPD-B1. Our results demonstrate that VRN1 and PPD1 alleles of varying strength allow fine tuning of flowering time in diverse winter wheat growing environments.
Project description:Heading of cereals is determined by complex genetic and environmental factors in which genes responsible for vernalization and photoperiod sensitivity play a decisive role. Our aim was to use diagnostic molecular markers to determine the main allele types in <i>VRN</i>-<i>A1</i>, <i>VRN</i>-<i>B1</i>, <i>VRN</i>-<i>D1</i>, <i>PPD</i>-<i>B1</i> and <i>PPD</i>-<i>D1</i> in a worldwide wheat collection of 683 genotypes and to investigate the effect of these alleles on heading in the field. The dominant <i>VRN</i>-<i>A1</i>, <i>VRN</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i> alleles were present at a low frequency. The <i>PPD</i>-<i>D1a</i> photoperiod-insensitive allele was carried by 57 % of the cultivars and was most frequent in Asian and European cultivars. The <i>PPD</i>-<i>B1</i> photoperiod-insensitive allele was carried by 22 % of the genotypes from Asia, America and Europe. Nine versions of the <i>PPD</i>-<i>B1</i>-insensitive allele were identified based on gene copy number and intercopy structure. The allele compositions in <i>PPD</i>-<i>D1</i>, <i>PPD</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i> significantly influenced heading and together explained 37.5 % of the phenotypic variance. The role of gene model increased to 39.1 % when <i>PPD</i>-<i>B1</i> intercopy structure was taken into account instead of overall <i>PPD</i>-<i>B1</i> type (sensitive vs. insensitive). As a single component, <i>PPD</i>-<i>D1</i> had the most important role (28.0 % of the phenotypic variance), followed by <i>PPD</i>-<i>B1</i> (12.3 % for <i>PPD</i>-<i>B1</i>_overall, and 15.1 % for <i>PPD</i>-<i>B1</i>_intercopy) and <i>VRN</i>-<i>D1</i> (2.2 %). Significant gene interactions were identified between the marker alleles within <i>PPD</i>-<i>B1</i> and between <i>VRN</i>-<i>D1</i> and the two <i>PPD1</i> genes. The earliest heading genotypes were those with the photoperiod-insensitive allele in <i>PPD</i>-<i>D1</i> and <i>PPD</i>-<i>B1</i>, and with the spring allele for <i>VRN</i>-<i>D1</i> and the winter alleles for <i>VRN</i>-<i>A1</i> and <i>VRN</i>-<i>B1</i>. This combination could only be detected in genotypes from Southern Europe and Asia. Late-heading genotypes had the sensitivity alleles for both <i>PPD1</i> genes, regardless of the allelic composition of the <i>VRN1</i> genes. There was a 10-day difference in heading between the earliest and latest groups under field conditions.
Project description:A total of 205 wheat cultivars from the Yellow and Huai valley of China were used to identify allelic variations of vernalization and photoperiod response genes, as well as the copy number variations (CNVs) of Ppd-B1 and Vrn-A1 genes. A novel Vrn-D1 allele with 174-bp insertion in the promoter region of the recessive allele vrn-D1 was discovered in three Chinese wheat cultivars and designated as Vrn-D1c. Quantitative real-time polymerase chain reaction showed that cultivars with the Vrn-D1c allele exhibited significantly higher expression of the Vrn-D1 gene than that in cultivars with the recessive allele vrn-D1, indicating that the 174-bp insertion of Vrn-D1c contributed to the increase in Vrn-D1 gene expression and caused early heading and flowering. The five new cis-elements (Box II-like, 3-AF1 binding site, TC-rich repeats, Box-W1 and CAT-box) in the 174-bp insertion possibly promoted the basal activity level of Vrn-D1 gene. Two new polymorphism combinations of photoperiod genes were identified and designated as Ppd-D1_Hapl-IX and Ppd-D1_Hapl-X. Association of the CNV of Ppd-B1 gene with the heading and flowering days showed that the cultivars with Ppd-B1_Hapl-VI demonstrated the earliest heading and flowering times, and those with Ppd-B1_Hapl-IV presented the latest heading and flowering times in three cropping seasons. Distribution of the vernalization and photoperiod response genes indicated that all recessive alleles at the four vernalization response loci, Ppd-B1_Hapl-I at Ppd-B1 locus, and Ppd-D1_Hapl-I at the Ppd-D1 locus were predominant in Chinese winter wheat cultivars. This study can provide useful information for wheat breeding programs to screen wheat cultivars with relatively superior adaptability and maturity.
Project description:Heading date in wheat (Triticum aestivum L.) and other small grain cereals is affected by the vernalization and photoperiod pathways. The reduced-height loci also have an effect on growth and development. Heading date, which occurs just prior to anthesis, was evaluated in a population of 299 hard winter wheat entries representative of the U.S. Great Plains region, grown in nine environments during 2011-2012 and 2012-2013. The germplasm was evaluated for candidate genes at vernalization (Vrn-A1, Vrn-B1, and Vrn-D1), photoperiod (Ppd-A1, Ppd-B1 and Ppd-D1), and reduced-height (Rht-B1 and Rht-D1) loci using polymerase chain reaction (PCR) and Kompetitive Allele Specific PCR (KASP) assays. Our objectives were to determine allelic variants known to affect flowering time, assess the effect of allelic variants on heading date, and investigate changes in the geographic and temporal distribution of alleles and haplotypes. Our analyses enhanced understanding of the roles developmental genes have on the timing of heading date in wheat under varying environmental conditions, which could be used by breeding programs to improve breeding strategies under current and future climate scenarios. The significant main effects and two-way interactions between the candidate genes explained an average of 44% of variability in heading date at each environment. Among the loci we evaluated, most of the variation in heading date was explained by Ppd-D1, Ppd-B1, and their interaction. The prevalence of the photoperiod sensitive alleles Ppd-A1b, Ppd-B1b, and Ppd-D1b has gradually decreased in U.S. Great Plains germplasm over the past century. There is also geographic variation for photoperiod sensitive and reduced-height alleles, with germplasm from breeding programs in the northern Great Plains having greater incidences of the photoperiod sensitive alleles and lower incidence of the semi-dwarf alleles than germplasm from breeding programs in the central or southern plains.
Project description:The major physiological determinants of wheat (Triticum aestivum L.) phenology in a given area are a response to vernalization temperature and day length, which are at least in part, regulated by the allelic variation at the vernalization (VRN) and photoperiod (PPD) loci, respectively. Characterization of the existing genetic variation for plant phenology in winter wheat can assist breeding programs improve adaptation to local environments and to optimize wheat phenology for the changing climate. The objectives of this research were to characterize the allelic variation at the major VRN and PPD loci in a diverse panel of high latitude winter wheat genotypes (n = 203) and to associate the allelic variation with phenologic, agronomic and adaptation traits. The panel was genotyped using allele-specific markers at vernalization (VRN-A1, VRN-B1, VRN-D1 and VRN-B3) and photoperiod (PPD-A1, PPD-B1, and PPD-D1) loci and phenotyped for agronomically-important traits. Though photoperiod sensitivity was more prevalent, most of the variation in the phenology of the winter wheat panel was explained by allelic variation at PPD-D1, PPD-A1, and the interaction between these loci. While a typical high latitude winter wheat genotype is one that carries winter alleles at all major VRN loci and photoperiod sensitive alleles at the major PPD loci, in lower latitudes where winters are milder, the presence of one or two photoperiod insensitive alleles seems to contribute to higher yield and wider adaptation.
Project description:The <i>VERNALIZATION1</i> (<i>VRN1</i>) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of <i>VRN1</i> homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of <i>VRN1</i> homoeologs (<i>VRN</i>-<i>A1</i>, <i>VRN</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i>). We performed an in-depth sequence analysis of <i>VRN1</i> homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele <i>Vrn</i>-<i>B1f</i> with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the <i>Vrn</i>-<i>A1b</i> allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of <i>VRN1</i> homoeologs showed that <i>VRN</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i> are present in only one copy. The copy number of recessive <i>vrn</i>-<i>A1</i> ranged from one to four, while that of dominant <i>Vrn</i>-<i>A1</i> was one or two. Different numbers of <i>Vrn</i>-<i>A1a</i> copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more <i>vrn</i>-<i>A1</i> copies.
Project description:<h4>Background</h4>The precise identification of Winterness/Springness (growth habit) for bread wheat, which is determined by genes involved in vernalization and photoperiod, will contribute to the effective utilization of bread wheat varieties. Here, 198 varieties from the Yellow and Huai wheat production region (YHW) in China were collected to identify their vernalization (Vrn-1) and photoperiod (Ppd-1) gene composition via a series of functional markers and their association with vernalization and photoperiod requirements at three locations during two years of experiments. The growth habits were measured during the spring sowing season.<h4>Results</h4>The results showed that the semi-winter varieties (grades1-4) were most prevalent in the population. The relative effects of single Vrn alleles on the growth period, such as heading date (HD) and/or flowering date (FD), were as follows: Vrn-B1b?>?Vrn-B1a?>?Vrn-D1b?>?Vrn-D1a?>?vrn-D1?=?vrn-B1. The interactive effects of Vrn-B1 and Vrn-D1 on HD and FD were identical to those of Vrn-B1b. Approximately 35.3% of the cultivars carried Ppd-B1a (photoperiod-insensitive) and exhibited the earliest HD and FD. The Ppd-D1a-insensitive allele (Hapl II) was carried by just 0.5% of the varieties; however, the other two sensitive alleles were present at a higher frequency, and their effects were slightly weaker than those of Ppd-B1a. In addition, strong interactive effects between Ppd-B1 and Ppd-D1 were detected. In terms of mean values among various genotypes, the effects followed the order of Vrn-1?>?Ppd-1.<h4>Conclusions</h4>According to the results of ANOVA and least significant range (LSR) tests, we can conclude that Vrn-1 rather than Ppd-1 played a major role in controlling vernalization and photoperiod responses in this region. This research will be helpful for precisely characterizing and evaluating the HD, FD and even growth habit of varieties in the YHW at molecular levels.
Project description:BACKGROUND:Understanding the genetic basis of frost tolerance (FT) in wheat (Triticum aestivum L.) is essential for preventing yield losses caused by frost due to cellular damage, dehydration and reduced metabolism. FT is a complex trait regulated by a number of genes and several gene families. Availability of the wheat genomic sequence opens new opportunities for exploring candidate genes diversity for FT. Therefore, the objectives of this study were to identity SNPs and insertion-deletion (indels) in genes known to be involved in frost tolerance and to perform association genetics analysis of respective SNPs and indels on FT. RESULTS:Here we report on the sequence analysis of 19 candidate genes for FT in wheat assembled using the Chinese Spring IWGSC RefSeq v1.0. Out of these, the tandem duplicated C-repeat binding factors (CBF), i.e. CBF-A3, CBF-A5, CBF-A10, CBF-A13, CBF-A14, CBF-A15, CBF-A18, the vernalisation response gene VRN-A1, VRN-B3, the photoperiod response genes PPD-B1 and PPD-D1 revealed association to FT in 235 wheat cultivars. Within six genes (CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1) amino acid (AA) substitutions in important protein domains were identified. The amino acid substitution effect in VRN-A1 on FT was confirmed and new AA substitutions in CBF-A3, CBF-A15, VRN-B3, PPD-B1 and PPD-D1 located at highly conserved sites were detected. Since these results rely on phenotypic data obtained at five locations in 2 years, detection of significant associations of FT to AA changes in CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1 may be exploited in marker assisted breeding for frost tolerance in winter wheat. CONCLUSIONS:A set of 65 primer pairs for the genes mentioned above from a previous study was BLASTed against the IWGSC RefSeq resulting in the identification of 39 primer combinations covering the full length of 19 genes. This work demonstrates the usefulness of the IWGSC RefSeq in specific primer development for highly conserved gene families in hexaploid wheat and, that a candidate gene association genetics approach based on the sequence data is an efficient tool to identify new alleles of genes important for the response to abiotic stress in wheat.
Project description:BACKGROUND: Flowering time greatly influences the adaptation of wheat cultivars to diverse environmental conditions and is mainly controlled by vernalization and photoperiod genes. In wheat cultivars from the Yellow and Huai Valleys, which represent 60%-70% of the total wheat production in China, the large-scale genotyping of wheat germplasms has not yet been performed in terms of vernalization and photoperiod response alleles, limiting the use of Chinese wheat germplasms to a certain extent. RESULTS: In this study, 173 winter wheat cultivars and 51 spring wheat cultivars from China were used to identify allelic variations of vernalization and photoperiod genes as well as copy number variations of Ppd-B1 and Vrn-A1. Two new co-dominant markers were developed in order to more precisely examine Vrn-A1b, Vrn-B1a, and Vrn-B1b. Two novel alleles at the Vrn-B3 locus were discovered and were designated Vrn-B3b and Vrn-B3c. Vrn-B3b had an 890-bp insertion in the promoter region of the recessive vrn-B3 allele, and Vrn-B3c allele had 2 deletions (a 20-bp deletion and a 4-bp deletion) in the promoter region of the dominant Vrn-B3a allele. Cultivar Hemai 26 lacked the Vrn-A1 gene. RT-PCR indicated that the 890-bp insertion in the Vrn-B3b allele significantly reduced the transcription of the Vrn-B3 gene. Cultivars Chadianhong with the Vrn-B3b allele and Hemai 26 with a Vrn-A1-null allele possessed relatively later heading and flowering times compared to those of Yanzhan 4110, which harbored recessive vrn-B3 and vrn-A1 alleles. Through identification of photoperiod genes, 2 new polymorphism combinations were found in 6 winter wheat cultivars and were designated Hapl-VII and Hapl-VIII, respectively. Distribution of the vernalization and photoperiod genes indicated that all recessive alleles at the 4 vernalization response loci, truncated "Chinese Spring" Ppd-B1 allele at Ppd-B1 locus and Hapl-I at the Ppd-D1 locus were predominant in Chinese winter wheat cultivars. CONCLUSION: This study illustrated the distribution of vernalization and photoperiod genes and identified 2 new Vrn-B3 alleles, 1 Vrn-A1-null allele, and two new Ppd-D1 polymorphism combinations, using developed functional markers. Results of this study have the potential to provide useful information for screening relatively superior wheat cultivars for better adaptability and maturity.
Project description:Triticum aestivum L. cv 'Chogokuwase' is an extra-early flowering common wheat cultivar that is insensitive to photoperiod conferred by the photoperiod insensitive alleles at the Photoperiod-B1 (Ppd-B1) and Ppd-D1loci, and does not require vernalization for flowering. This reduced vernalization requirement is likely due to the spring habitat allele Vrn-D1 at the VERNALIZATION-D1 locus. Genotypes of the Ppd-1 loci that determine photoperiod sensitivity do not fully explain the insensitivity to photoperiod seen in 'Chogokuwase'. We detected altered expression patterns of clock and clock-output genes including Ppd-1 in 'Chogokuwase' that were similar to those in an einkorn wheat mutant that lacks the clock-gene homologue, wheat PHYTOCLOCK 1 (WPCL1). Presumptive loss-of-function mutations in all WPCL1 homoeologous genes were found in 'Chogokuwase' and 'Geurumil', one of the parental cultivars. Segregation analysis of the two intervarietal F2 populations revealed that all the examined F2 plants that headed as early as 'Chogokuwase' had the loss-of-function wpcl1 alleles at all three homoeoloci. Some F2 plants carrying the wpcl1 alleles at three homoeoloci headed later than 'Chogokuwase', suggesting the presence of other loci influencing heading date. Flowering repressor Vrn-2 was up-regulated in 'Chogokuwase' and 'Geurumil' that had the triple recessive wpcl1 alleles. An elevated transcript abundance of Vrn-2 could explain the observation that 'Geurumil' and some F2 plants carrying the three recessive wpcl1 homeoealleles headed later than 'Chogokuwase'. In spite of the up-regulation of Vrn-2, 'Chogokuwase' may have headed earlier due to unidentified earliness genes. Our observations indicated that loss-of-function mutations in the clock gene wpcl1 are necessary but are not sufficient to explain the extra-early heading of 'Chogokuwase'.