A high-density genetic linkage map of Aegilops tauschii, the D-genome progenitor of bread wheat

 Aegilops tauschii is the diploid D-genome progenitor of bread wheat (Triticum aestivum L. em Thell, 2n=6x=42, AABBDD). A genetic linkage map of the Ae. tauschii genome was constructed, composed of 546 loci. One hundred and thirty two loci (24%) gave distorted segregation ratios. Sixty nine probes (13%) detected multiple copies in the genome. One hundred and twenty three of the 157 markers shared between the Ae. tauschii genetic and T. aestivum physical maps were colinear. The discrepancy in the order of five markers on the Ae. tauschii 3DS genetic map versus the T. aestivum 3D physical map indicated a possible inversion. Further work is needed to verify the discrepancies in the order of markers on the 4D, 5D and 7D Ae. tauschii genetic maps versus the physical and genetic maps of T. aestivum. Using common markers, 164 agronomically important genes were assigned to specific regions on Ae. tauschii linkage, and T. aestivum physical, maps. This information may be useful for map-based cloning and marker-assisted plant breeding. Received: 23 March 1998 / Accepted: 27 October 1998     

Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication

The domestication of wheat was instrumental in spawning the civilization of humankind, and it occurred through genetic mutations that gave rise to types with non-fragile rachises, soft glumes, and free-threshing seed. Wild emmer (Triticum turgidum ssp. dicoccoides), the tetraploid AB-genome progenitor of domesticated wheat has genes that confer tenacious glumes (Tg) that underwent genetic mutations to give rise to free-threshing wheat. Here, we evaluated disomic substitution lines involving chromosomes 2A and 2B of wild emmer accessions substituted for homologous chromosomes in tetraploid and hexaploid backgrounds. The results suggested that both chromosomes 2A and 2B of wild emmer possess genes that inhibit threshability. A population of recombinant inbred lines derived from the tetraploid durum wheat variety Langdon crossed with a Langdon — T. turgidum ssp. dicoccoides accession PI 481521 chromosome 2B disomic substitution line was used to develop a genetic linkage map of 2B, evaluate the genetics of threshability, and map the gene derived from PI 481521 that inhibited threshability. A 2BS linkage map comprised of 58 markers was developed, and markers delineated the gene to a 2.3 cM interval. Comparative analysis with maps containing the tenacious glume gene Tg-D1 on chromosome arm 2DS from Aegilops tauschii, the D genome progenitor of hexaploid wheat, revealed that the gene inhibiting threshability in wild emmer was homoeologous to Tg-D1 and therefore designated Tg-B1. Comparative analysis with rice and Brachypodium distachyon indicated a high level of divergence and poorly conserved colinearity, particularly near the Tg-B1 locus. These results provide a foundation for further studies involving Tg-B1, which, together with Tg-D1, had profound influences on wheat domestication.     

Patterns and impacting factors of gene evolutionary rate between wild and cultivated emmer wheat (Triticum turgidum)

Tetraploid emmer wheat (Triticum turgidum L., BBAA) is the founder progenitor of bread wheat, providing the valuable genetic resource and gene pool for wheat improvement. However, the evolutionary trajectory of tetraploid wheat, especially the evolutionary fate of different types of genes has not been well studied. In this study, the rate of non-synonymous substitution (d_N) and synonymous substitution (d_S) was calculated by comparing the orthologs between the wild emmer and cultivated durum wheat at the whole genome and subgenome levels to obtain the positively selected genes (PSGs) and negatively selected genes (NSGs). Then, mutation rate, gene length, exon number, GC content, codon bias, and expression level were comprehensively investigated and compared between the PSGs and NSGs. Within both wild emmer and cultivated durum wheat, PSGs between A and B subgenome displayed shorter gene and exon lengths as well as fewer exon numbers compared with NSGs, whereas from wild emmer to cultivated durum wheat, PSGs showed longer gene length and more exon numbers. Furthermore, PSGs displayed much higher expression levels and stronger codon usage bias, but lower genetic diversity compared with NSGs. Finally, two PSGs TdER1-6B, and TdLC7-2A, were found to play the crucial roles in regulating grain width and plant height of tetraploid wheat, respectively. This study systematically investigated the evolutionary, structural, and functional difference between PSGs and NSGs in tetraploid wheat, which will contribute to a better understanding of the selective mode and evolutionary trajectory during wheat domestication and evolution.     

Durum wheat as a candidate for the unknown female progenitor of bread wheat: an empirical study with a highly fertile F<Subscript>1</Subscript> hybrid with <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss.

Hexaploid bread wheat was derived from a hybrid cross between a cultivated form of tetraploid Triticum wheat (female progenitor) and a wild diploid species, Aegilops tauschii Coss. (male progenitor). This cross produced a fertile triploid F₁ hybrid that set hexaploid seeds. The identity of the female progenitor is unknown, but various cultivated tetraploid Triticum wheats exist today. Genetic and archaeological evidence suggests that durum wheat (T. turgidum ssp. durum) may be the female progenitor. In previous studies, however, F₁ hybrids of durum wheat crossed with Ae. tauschii consistently had low levels of fertility. To establish an empirical basis for the theory of durum wheat being the female progenitor of bread wheat, we crossed a durum wheat cultivar that carries a gene for meiotic restitution with a line of Ae. tauschii. F₁ hybrids were produced without using embryo rescue techniques. These triploid F₁ hybrids were highly fertile and spontaneously set hexaploid F₂ seeds at the average selfed seedset rate of 51.5%. To the best of our knowledge, this is the first example of the production of highly fertile F₁ hybrids between durum wheat and Ae. tauschii. The F₁ and F₂ hybrids are both similar morphologically to bread wheat and have vigorous growth habits. Cytological analyses of F₁ male gametogenesis showed that meiotic restitution is responsible for the high fertility of the triploid F₁ hybrids. The implications of these findings for the origin of bread wheat are discussed.     

Integration of dinucleotide microsatellites from hexaploid bread wheat into a genetic linkage map of durum wheat

 Seventy nine microsatellite markers from hexaploid bread wheat (T. aestivum L.) were integrated into a genetic linkage map of durum wheat (T. turgidum ssp. durum (Desf.) Huns.) created by RFLP segregation data from a population of 65 recombinant inbred lines. The results indicate a relatively even distribution of microsatellite loci and demonstrate that microsatellite markers from hexaploid wheat provide an excellent source of molecular markers for use in the genetics and breeding of durum wheat. Received: 16 July 1998 / Accepted: 13 October 1998     

Polyphenol oxidase (PPO) in wheat and wild relatives: molecular evidence for a multigene family

Wheat polyphenol oxidase (PPO) is the major cause of browning reactions that discolor Asian noodles and other wheat products. It has been hypothesized that genes encoding wheat PPOs may have evolved by gene duplication into a multigene family. Here we characterized PPO genomic sequences from diploid (Triticum monococcum, T. urartu, Aegilops tauschii, and Ae. speltoides), tetraploid (T. turgidum, subspecies dicoccoides and durum) and hexaploid (T. aestivum cultivars Klasic and ID377s) wheat species to gain a better understanding of the structure and organization of PPO genes. DNA fragments were amplified from a highly polymorphic and phylogenetic informative region of the gene. As a result, we obtained highly discriminative sequences. Three distinct PPOs, obtained from the A genome of T. monococcum, provided evidence for gene duplication events (paralogous loci). Furthermore, the number of sequences obtained for bread and durum wheat was higher than the expected number of orthologous loci. Sequence comparison revealed nucleotide and structural diversity, and detected five sequence intron types, all with a common insertion position. This was hypothesized to be homologous to that of intron 2 of previously reported wheat PPOs. A MITE of the Stowaway family accounted for the major difference between the five intervening sequences, and was unique to T. aestivum cv. Klasic. Nucleotide and structural diversity, together with well-resolved phylogenetic trees, provided molecular evidence to support the hypothesis of a PPO multigene family structure and organization. Mention of trademark or proprietary products does not constitute a guarantee or warranty of a product by the US Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable. This article is in the public domain and not copyrightable.     

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication‐related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.     

Wheat domestication: lessons for the future

Wheat was one of the first crops to be domesticated more than 10,000 years ago in the Middle East. Molecular genetics and archaeological data have allowed the reconstruction of plausible domestication scenarios leading to modern cultivars. For diploid einkorn and tetraploid durum wheat, a single domestication event has likely occurred in the Karacadag Mountains, Turkey. Following a cross between tetraploid durum and diploid T.?tauschii, the resultant hexaploid bread wheat was domesticated and disseminated around the Caucasian region. These polyploidisation events facilitated wheat domestication and created genetic bottlenecks, which excluded potentially adaptive alleles. With the urgent need to accelerate genetic progress to confront the challenges of climate change and sustainable agriculture, wild ancestors and old landraces represent a reservoir of underexploited genetic diversity that may be utilized through modern breeding methods. Understanding domestication processes may thus help identifying new strategies.     

Wheat genetic diversity trends during domestication and breeding

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheats genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm.     

Domesticated emmer wheat [T. turgidum L. subsp. dicoccon (Schrank) Thell.] as a source for improvement of zinc efficiency in durum wheat

Modern durum wheat (AABB) is more sensitive to zinc (Zn) deficiency than bread wheat (AABBDD). One strategy to increase productivity and expansion of durum wheat industry in Zn-deficient soils is to improve its ability to grow and yield in such soils. This ability is termed Zn efficiency. In a growth room experiment using soil culture, we assessed the potential of Triticum turgidum L. subsp. dicoccon (Shrank) Thell. (domesticated emmer wheat, AABB) as a genetic resource for further improvement of Zn efficiency in modern durum wheat. Twenty four accessions of domesticated emmer wheat, four durum landraces/cultivars, and two bread wheat cultivars/ advanced breeders lines of known Zn efficiency were tested under Zn deficiency and Zn sufficiency. Significant variation was observed among genotypes in Zn deficiency symptoms, dry matter production, shoot Zn concentration, shoot Zn content and Zn utilisation efficiency (physiological efficiency). We identified domesticated emmer wheat accessions with greater Zn efficiency than modern durum wheat and even bread wheat genotypes. These accessions could be used in breeding programs to improve Zn efficiency of durum wheat. The results suggest that Zn efficiency of durum or bread wheat is likely to be determined collectively by its progenitors.     

High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis

Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F₆ hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.     

Introgression of wheat DNA markers from A, B and D genomes in early generation progeny of Aegilops cylindrica Host × Triticum aestivum L. hybrids

Introgression from allohexaploid wheat (Triticum aestivum L., AABBDD) to allotetraploid jointed goatgrass (Aegilops cylindrica Host, CCDD) can take place in areas where the two species grow in sympatry and hybridize. Wheat and Ae. cylindrica share the D genome, issued from the common diploid ancestor Aegilops tauschii Coss. It has been proposed that the A and B genome of bread wheat are secure places to insert transgenes to avoid their introgression into Ae. cylindrica because during meiosis in pentaploid hybrids, A and B genome chromosomes form univalents and tend to be eliminated whereas recombination takes place only in D genome chromosomes. Wheat random amplified polymorphic DNA (RAPD) fragments, detected in intergeneric hybrids and introgressed to the first backcross generation with Ae. cylindrica as the recurrent parent and having a euploid Ae. cylindrica chromosome number or one supernumerary chromosome, were assigned to wheat chromosomes using Chinese Spring nulli-tetrasomic wheat lines. Introgressed fragments were not limited to the D genome of wheat, but specific fragments of A and B genomes were also present in the BC1. Their presence indicates that DNA from any of the wheat genomes can introgress into Ae. cylindrica. Successfully located RAPD fragments were then converted into highly specific and easy-to-use sequence characterised amplified regions (SCARs) through sequencing and primer design. Subsequently these markers were used to characterise introgression of wheat DNA into a BC1S1 family. Implications for risk assessment of genetically modified wheat are discussed.     

AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat (<Emphasis Type="Italic">T. turgidum</Emphasis> ssp. <Emphasis Type="Italic">dicoccoides </Emphasis> × <Emphasis Type="Italic">T. tauschii</Emphasis>) as a source of favourable alleles for milling and baking quality traits

The advanced backcross QTL (AB-QTL) strategy was utilised to locate quantitative trait loci (QTLs) for baking quality traits in two BC₂F₃ populations of winter wheat. The backcrosses are derived from two German winter wheat cultivars, Batis and Zentos, and two synthetic, hexaploid wheat accessions, Syn022 and Syn086. The synthetics originate from hybridisations of wild emmer (T. turgidum spp. dicoccoides) and T. tauschii, rather than from durum wheat and T. tauschii and thus allowed for the first time to test for exotic QTL effects on wheat genomes A and B in addition to genome D. The investigated quality traits comprised hectolitre weight, grain hardness, flour yield Type 550, falling number, grain protein content, sedimentation volume and baking volume. One hundred and forty-nine SSR markers were applied to genotype a total of 400 BC₂F₃ lines. For QTL detection, a mixed-model ANOVA was conducted, including the effects DNA marker, BC₂F₃ line, environment and marker × environment interaction. Overall 38 QTLs significant for a marker main effect were detected. The exotic allele improved trait performance at 14 QTLs (36.8%), while the elite genotype contributed the favourable effect at 24 QTLs (63.2%). The favourable exotic alleles were mainly associated with grain protein content, though the greatest improvement of trait performance due to the exotic alleles was achieved for the traits falling number and sedimentation volume. At the QTL on chromosome 4B the exotic allele increased the falling number by 19.6% and at the QTL on chromosome 6D the exotic allele led to an increase of the sedimentation volume by 21.7%. The results indicate that synthetic wheat derived from wild emmer × T. tauschii carries favourable QTL alleles for baking quality traits, which might be useful for breeding improved wheat varieties by marker-assisted selection.     

Additive genetic variance and covariance between relatives in synthetic wheat crosses with variable parental ploidy levels

Cultivated bread wheat (Triticum aestivum L.) is an allohexaploid species resulting from the natural hybridization and chromosome doubling of allotetraploid durum wheat (T. turgidum) and a diploid goatgrass Aegilops tauschii Coss (Ae. tauschii). Synthetic hexaploid wheat (SHW) was developed through the interspecific hybridization of Ae. tauschii and T. turgidum, and then crossed to T. aestivum to produce synthetic hexaploid wheat derivatives (SHWDs). Owing to this founding variability, one may infer that the genetic variances of native wild populations vs improved wheat may vary due to their differential origin and evolutionary history. In this study, we partitioned the additive variance of SHW and SHWD with respect to their breed origin by fitting a hierarchical Bayesian model with heterogeneous covariance structure for breeding values to estimate variance components for each breed category, and segregation variance. Two data sets were used to test the proposed hierarchical Bayesian model, one from a multi-year multi-location field trial of SHWD and the other comprising the two species of SHW. For the SHWD, the Bayesian estimates of additive variances of grain yield from each breed category were similar for T. turgidum and Ae. tauschii, but smaller for T. aestivum. Segregation variances between Ae. tauschii—T. aestivum and T. turgidum—T. aestivum populations explained a sizable proportion of the phenotypic variance. Bayesian additive variance components and the Best Linear Unbiased Predictors (BLUPs) estimated by two well-known software programs were similar for multi-breed origin and for the sum of the breeding values by origin for both data sets. Our results support the suitability of models with heterogeneous additive genetic variances to predict breeding values in wheat crosses with variable ploidy levels.     

Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Key message

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement.

Abstract

Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today’s fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.     

Identification and genetic characterization of an <Emphasis Type="Italic">Aegilops tauschii</Emphasis> ortholog of the wheat leaf rust disease resistance gene <Emphasis Type="Italic">Lr1</Emphasis>

Aegilops tauschii (goat grass) is the progenitor of the D genome in hexaploid bread wheat. We have screened more than 200 Ae. tauschii accessions for resistance against leaf rust (Puccinia triticina) isolates, which are avirulent on the leaf rust resistance gene Lr1. Approximately 3.5% of the Ae. tauschii accessions displayed the same low infection type as the tester line Thatcher Lr1. The accession Tr.t. 213, which showed resistance after artificial infection with Lr1 isolates both in Mexico and in Switzerland, was chosen for further analysis. Genetic analysis showed that the resistance in this accession is controlled by a single dominant gene, which mapped at the same chromosomal position as Lr1 in wheat. It was delimited in a 1.3-cM region between the restriction fragment length polymorphism (RFLP) markers ABC718 and PSR567 on chromosome 5DL of Ae. tauschii. The gene was more tightly linked to PSR567 (0.47 cM) than to ABC718 (0.79 cM). These results indicate that the resistance gene in Ae. tauschii accession Tr.t. 213 is an ortholog of the leaf rust resistance gene Lr1 of bread wheat, suggesting that Lr1 originally evolved in diploid goat grass and was introgressed into the wheat D genome during or after domestication of hexaploid wheat. Compared to hexaploid wheat, higher marker polymorphism and recombination frequencies were observed in the region of the Lr1 ortholog in Ae. tauschii. The identification of Lr1^Ae, the orthologous gene of wheat Lr1, in Ae. tauschii will allow map-based cloning of Lr1 from this genetically simpler, diploid genome.Hong-Qing Ling and Jiwen Qiu have contributed equally to this work     

GluDy allele variations in Aegilops tauschii and Triticum aestivum: implications for the origins of hexaploid wheats

To investigate the evolution and geographical origins of hexaploid wheat, we examined a 284 bp sequence from the promoter region of the GluDy locus, coding for the y subunit of high-molecular-weight glutenin. Fourteen different alleles were found in 100 accessions of Aegilops tauschii and 169 of Triticum aestivum. Two alleles were present in both species; the other 7 alleles from Ae. tauschii and 5 from T. aestivum were unique to their respective species. The two shared alleles differed at only one nucleotide position within the region sequenced, but their apparent association with the common haplotypes GluD1a and GluD1d, which have substantial differences within their GluDy coding regions, makes it unlikely that the alleles evolved independently in Ae. tauschii and T. aestivum. The results therefore support previous studies which suggest that there were at least two Ae. tauschii sources that contributed germplasm to the D genome of T. aestivum. The number of alleles present in T. aestivum, and the nucleotide diversity of these alleles, indicates that this region of the D genome has undergone relatively rapid change since polyploidisation. Ae. tauschii from Syria and Turkey had relatively high nucleotide diversity and possessed all the major GluDy alleles, indicating that these populations are probably ancient and not the result of adventive spread. The presence in the Turkish population of both of the shared alleles suggests that hexaploid wheat is likely to have originated in southeast Turkey or northern Syria, within the Fertile Crescent and near to the farming villages at which archaeological remains of hexaploid wheats are first found. A second, more recent, hexaploidisation probably occurred in Iran.