Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

Mapping Intimacies ◽

10.1101/855106 ◽

2019 ◽

Cited By ~ 1

Author(s):

Moses Nyine ◽

Elina Adhikari ◽

Marshall Clinesmith ◽

Katherine W. Jordan ◽

Allan K. Fritz ◽

...

Keyword(s):

Aegilops Tauschii ◽

Allelic Diversity ◽

Sequence Divergence ◽

Snp Markers ◽

D Genome ◽

Entire Genome ◽

Wild Allele ◽

Negative Epistasis ◽

The Hill ◽

Genomic Patterns

AbstractIntrogression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop imrpovement to ensure retention of introgressed diversity across entire genome.

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Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401479 ◽

2020 ◽

Vol 10 (10) ◽

pp. 3651-3661 ◽

Cited By ~ 1

Author(s):

Moses Nyine ◽

Elina Adhikari ◽

Marshall Clinesmith ◽

Katherine W. Jordan ◽

Allan K. Fritz ◽

...

Keyword(s):

Crop Improvement ◽

Aegilops Tauschii ◽

Allelic Diversity ◽

Sequence Divergence ◽

Snp Markers ◽

D Genome ◽

Entire Genome ◽

Wild Allele ◽

The Hill ◽

Genomic Patterns

Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.

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Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance

Functional Plant Biology ◽

10.1071/fp12083 ◽

2012 ◽

Vol 39 (7) ◽

pp. 569 ◽

Cited By ~ 12

Author(s):

Hollie Webster ◽

Gabriel Keeble ◽

Bernard Dell ◽

John Fosu-Nyarko ◽

Y. Mukai ◽

...

Keyword(s):

Cell Wall ◽

Drought Tolerance ◽

Aegilops Tauschii ◽

Sequence Divergence ◽

Wheat Chromosome ◽

Triticum Aestivum L ◽

Pollen Sterility ◽

Cell Wall Invertase ◽

D Genome ◽

Specific Expression

In wheat (Triticum aestivum L.) drought-induced pollen sterility is a major contributor to grain yield loss and is caused by the downregulation of the cell wall invertase gene IVR1. The IVR1 gene catalyses the irreversible hydrolysis of sucrose to glucose and fructose, the essential energy substrates which support pollen development. Downregulation of IVR1 in response to drought is isoform specific and shows variation in temporal and tissue-specific expression. IVR1 is now prompting interest as a candidate gene for molecular marker development to screen wheat germplasm for improved drought tolerance. The aim of this study was to define the family of IVR1 genes to enable: (1) individual isoforms to be assayed in gene expression studies; and (2) greater accuracy in IVR1 mapping to the wheat genetic map and drought tolerance QTL analysis. Using a cell wall invertase-specific motif as a probe, wheat genomics platforms were screened for the presence of unidentified IVR1 isoforms. Wheat genomics platforms screened included the IWGSC wheat survey sequence, the wheat D genome donor sequence from Aegilops tauschii Coss, and the CCG wheat chromosome 3B assembly: contig506. Chromosome-specific sequences homologous to the query motif were isolated and characterised. Sequence annotation results showed five previously unidentified IVR1 isoforms exist on multiple chromosome arms and on all three genomes (A, B and D): IVR1–3A, IVR1–4A, IVR1–5B, IVR1.2–3B and IVR1-5D. Including three previously characterised IVR1 isoforms (IVR1.1–1A, IVR1.2–1A and IVR1.1–3B), the total number of isoform gene family members is eight. The IVR1 isoforms contain two motifs common to cell wall invertase (NDPN and WECPDF) and a high degree of conservation in exon 4, suggesting conservation of functionality. Sequence divergence at a primary structure level in other regions of the gene was evident amongst the isoforms, which likely contributes to variation in gene regulation and expression in response to water deficit within this subfamily of IVR1 isoforms in wheat.

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The D-genome plays a critical role in the formation of haploid Aegilops tauschii through Imperata cylindrica mediated uniparental chromosome elimination

The Nucleus ◽

10.1007/s13237-015-0151-2 ◽

2015 ◽

Vol 58 (3) ◽

pp. 199-206 ◽

Cited By ~ 4

Author(s):

Yasuhiko Mukai ◽

Gentatsu Okamoto ◽

Shiho Kiryu ◽

Satoru Takemoto ◽

Santosh Kumar Sharma ◽

...

Keyword(s):

Critical Role ◽

Aegilops Tauschii ◽

Chromosome Elimination ◽

Imperata Cylindrica ◽

D Genome

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Highly Recombinogenic Regions at Seed Storage Protein Loci on Chromosome 1DS of Aegilops tauschii, the D-Genome Donor of Wheat

Genetics ◽

10.1093/genetics/155.1.361 ◽

2000 ◽

Vol 155 (1) ◽

pp. 361-367 ◽

Cited By ~ 3

Author(s):

Wolfgang Spielmeyer ◽

Odile Moullet ◽

André Laroche ◽

Evans S Lagudah

Keyword(s):

Genetic Distance ◽

Storage Protein ◽

Seed Storage Protein ◽

Aegilops Tauschii ◽

Bac Library ◽

Seed Storage ◽

D Genome ◽

Rflp Map ◽

Genome Donor ◽

The Relationship

Abstract A detailed RFLP map was constructed of the distal end of the short arm of chromosome 1D of Aegilops tauschii, the diploid D-genome donor species of hexaploid wheat. Ae. tauschii was used to overcome some of the limitations commonly associated with molecular studies of wheat such as low levels of DNA polymorphism. Detection of multiple loci by most RFLP probes suggests that gene duplication events have occurred throughout this chromosomal region. Large DNA fragments isolated from a BAC library of Ae. tauschii were used to determine the relationship between physical and genetic distance at seed storage protein loci located at the distal end of chromosome 1DS. Highly recombinogenic regions were identified where the ratio of physical to genetic distance was estimated to be <20 kb/cM. These results are discussed in relation to the genome-wide estimate of the relationship between physical and genetic distance.

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TRANSFER AND MOLECULAR MAPPING OF AEGILOPS TAUSCHII-DERIVED HESSIAN FLY RESISTANCE GENES (H22, H23, H24, AND H26) FROM D GENOME OF TRITICUM AESTIVUM ONTO A GENOME CHROMOSOMES OF TRITICUM TURGIDUM BY INDUCED HOMOEOLOGOUS RECOMBINATION.

International Journal of Advanced Research ◽

10.21474/ijar01/5826 ◽

2017 ◽

Vol 5 (11) ◽

pp. 728-750

Author(s):

Moha Ferrahi ◽

◽

B Friebe ◽

JH Hatchett ◽

BS Gill ◽

...

Keyword(s):

Triticum Aestivum ◽

Resistance Genes ◽

Molecular Mapping ◽

Triticum Turgidum ◽

Aegilops Tauschii ◽

Hessian Fly ◽

Homoeologous Recombination ◽

D Genome ◽

Hessian Fly Resistance ◽

A Genome

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Evaluation of Aegilops tauschii (Coss.) germplasm for Karnal bunt resistance in a screen house with simulated environmental conditions

Plant Genetic Resources ◽

10.1017/s1479262108982654 ◽

2008 ◽

Vol 6 (02) ◽

pp. 79-84 ◽

Cited By ~ 6

Author(s):

Parveen Chhuneja ◽

Satinder Kaur ◽

Kuldeep Singh ◽

H. S. Dhaliwal

Keyword(s):

Host Plant ◽

Plant Resistance ◽

Environmental Conditions ◽

Host Plant Resistance ◽

Aegilops Tauschii ◽

Karnal Bunt ◽

Tilletia Indica ◽

D Genome ◽

Moderately Resistant ◽

Screen House

Karnal bunt (KB) of wheat, caused byTilletia indica(Mitra) Mundkur, adversely affects international wheat trading and the movement of germplasm between countries due to quarantine restrictions. Breeding for host plant resistance requires the identification of KB resistance sources. Accessions of the D genome progenitor of bread wheat,Aegilops tauschii, were screened in a specially designed screen-house, where the optimum environmental conditions conducive for KB development were simulated by controlling temperature, humidity, fogging and shading. The 183 accessions were subjected to artificial inoculation with a mixture of nine KB isolates, and seven proved highly resistant and four moderately resistant over three rounds of screening over 3 years.

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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Nature ◽

10.1038/nature24486 ◽

2017 ◽

Vol 551 (7681) ◽

pp. 498-502 ◽

Cited By ~ 230

Author(s):

Ming-Cheng Luo ◽

Yong Q. Gu ◽

Daniela Puiu ◽

Hao Wang ◽

Sven O. Twardziok ◽

...

Keyword(s):

Genome Sequence ◽

Aegilops Tauschii ◽

D Genome

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Comparative Mapping of Genes for Brittle Rachis in Triticum

Czech Journal of Genetics and Plant Breeding ◽

10.17221/3671-cjgpb ◽

2011 ◽

Vol 41 (No. 2) ◽

pp. 39-44 ◽

Cited By ~ 8

Author(s):

N. Watanabe ◽

N. Takesada ◽

Y. Fujii ◽

P. Martinek

Keyword(s):

Triticum Turgidum ◽

Aegilops Tauschii ◽

Dominant Gene ◽

Introgression Line ◽

Triticum Aestivum L ◽

Grass Species ◽

Brittle Rachis ◽

D Genome ◽

Adaptive Value ◽

Group 3

The brittle rachis phenotype is of adaptive value in wild grass species because it causes spontaneous spike shattering. The genes on the homoeologous group 3 chromosomes determine the brittle rachis in Triticeae. A few genotypes with brittle rachis have also been found in the cultivated Triticum. Using microsatellite markers, the homoeologous genes for brittle rachis were mapped in hexaploid wheat (Triticum aestivum L.), durum wheat (Triticum turgidum L. conv. durum /Desf./) and Aegilops tauschii Coss. On chromosome 3AS, the gene for brittle rachis, Br2, was linked with the centromeric marker, Xgwm32, at the distance of 13.3 cM. Br3 was located on chromosome 3BS and linked with the centromeric marker, Xgwm72 (14.2 cM). Br1 was located on chromosome 3DS. The distance from the centromeric marker Xgdm72 was 23.6 cM. The loci Br1, Br2 and Br3 determine disarticulation of rachides above the junction of the rachilla with the rachis so that a fragment of rachis is attached below each spikelet. The rachides of Ae. tauschii are brittle at every joint, so that the mature spike disarticulates into barrel type. The brittle rachis was determined by a dominant gene, Brt, which was linked to the centromeric marker, Xgdm72 (19.7 cM), on chromosome 3DS. A D-genome introgression line, R-61, was derived from the cross Bet Hashita/Ae. tauschii, whose rachis disarticulated as a wedge type. The gene for brittle rachis of R-61, tentatively designated as Br61, was distally located on chromosome 3DS, and was linked with the centromeric marker, Xgdm72 (27.5 cM). We discussed how the brittle rachis of R-61 originated genetically.

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Genetic variability of spelt factor gene in Triticum and Aegilops species

BMC Plant Biology ◽

10.1186/s12870-020-02536-8 ◽

2020 ◽

Vol 20 (S1) ◽

Author(s):

Valeriya Vavilova ◽

Irina Konopatskaia ◽

Alexandr Blinov ◽

Elena Ya. Kondratenko ◽

Yuliya V. Kruchinina ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Chinese Spring ◽

Stop Codon ◽

Aegilops Tauschii ◽

Premature Stop Codon ◽

Gene Sequences ◽

D Genome ◽

Factor Gene ◽

Spike Shape ◽

Wide Range

Abstract Background Threshability, rachis fragility and spike shape are critical traits for the domestication and evolution of wheat, determining the crop yield and efficiency of the harvest. Spelt factor gene Q controls a wide range of domestication-related traits in polyploid wheats, including those mentioned above. The main goal of the present study was to characterise the Q gene for uninvestigated accessions of wheats, including four endemics, and Aegilops accessions, and to analyze the species evolution based on differences in Q gene sequences. Results We have studied the spike morphology for 15 accessions of wheat species, including four endemics, namely Triticum macha, T. tibetanum, T. aestivum ssp. petropavlovskyi and T. spelta ssp. yunnanense, and 24 Aegilops accessions, which are donors of B and D genomes for polyploid wheat. The Q-5A, q-5D and q-5S genes were investigated, and a novel allele of the Q-5A gene was found in accessions of T. tibetanum (KU510 and KU515). This allele was similar to the Q allele of T. aestivum cv. Chinese Spring but had an insertion 161 bp in length within exon 5. This insertion led to a frameshift and premature stop codon formation. Thus, the T. tibetanum have spelt spikes, which is probably determined by the gene Tg, rather than Q. We determined the variability within the q-5D genes among hexaploid wheat and their D genome donor Aegilops tauschii. Moreover, we studied the accessions C21–5129, KU-2074, and K-1100 of Ae. tauschii ssp. strangulata, which could be involved in the origin of hexaploid wheats. Conclusions The variability and phylogenetic relationships of the Q gene sequences studied allowed us to clarify the relationships between species of the genus Triticum and to predict the donor of the D genome among the Ae. tauschii accessions. Ae. tauschii ssp. strangulata accessions C21–5129, KU-2074 and K-1100 are the most interesting among the analysed accessions, since their partial sequence of q-5D is identical to the q-5D of T. aestivum cv. Chinese Spring. This result indicates that the donor is Ae. tauschii ssp. strangulata but not Ae. tauschii ssp. tauschii. Our analysis allowed us to clarify the phylogenetic relationships in the genus Triticum.

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