Discovery of quantitative trait loci for crossability from a synthetic wheat genotype

[Molecular markers in the genetic analysis of crossability of bread wheat with rye]

Мягкая пшеница (Triticum aestivum L.), сорта которой широко используются в мировом про- изводстве зерна, плохо скрещивается с видами других родов Triticeae Dum., что ограничивает возмож- ности введения чужеродного генетического материала в ее генофонд и создания новых сортов, хорошо адаптированных к различным неблагоприятным абиотическим и биотическим факторам внешней среды. Известно, что скрещиваемость мягкой пшеницы с представителями других родов контролируется генами Kr1–Kr4 (Crossability with Rye, Hordeum and Aegilops spp.) и геном SKr (Suppressor of crossability). Из названных генов наиболее сильное влияние на признак оказывают SKr и Kr1. В рецессивном состоянии, когда гены не функционируют, может завязываться более 50 % зерновок от числа цветков в колосе при опылении пыль- цой чужеродного вида. Оба гена локализованы в хромосоме 5B. Расположение гена SKr в коротком плече хромосомы 5B ограничено маркерами GBR0233 и Xgwm234 в тесном сцеплении с маркерами Xcfb341, TGlc2 и gene12. Ген Kr1 расположен в длинном плече хромосомы 5B, проксимальнее гена Ph1, между EST-SSR- маркерами Xw5145 и Xw9340. Маркеры, разработанные для гена SKr, применяли для контроля переноса его рецессивного аллеля skr в другие генотипы мягкой пшеницы, что позволило получать формы с высокой за- вязываемостью гибридных зерновок при скрещивании с рожью. Однако в целом использование маркеров генов SKr и Kr1 в практической маркер-ориентированной селекции и молекулярном скрининге образцов ex situ коллекций изучено недостаточно. Большие перспективы в этом плане открывает определение пол- ной нуклеотидной последовательности гена Kr1 у контрастных по скрещиваемости сортов мягкой пшени- цы, это дает возможность создания внутригенных аллель-специфичных маркеров. В представленном обзо- ре рассмотрены генетические ресурсы, созданные посредством гибридизации мягкой пшеницы с рожью; вопросы географического распространения легко скрещивающихся форм пшеницы и генетического кон- троля совместимости пшеницы и ржи; достижения в использовании молекулярных маркеров в картирова- нии Kr-генов и контроле их передачи.

The Use of Pentaploid Crosses for the Introgression of Amblyopyrum muticum and D-Genome Chromosome Segments Into Durum Wheat

The wild relatives of wheat provide an important source of genetic variation for wheat improvement. Much of the work in the past aimed at transferring genetic variation from wild relatives into wheat has relied on the exploitation of the ph1b mutant, located on the long arm of chromosome 5B. This mutation allows homologous recombination to occur between chromosomes from related but different genomes, e.g. between the chromosomes of wheat and related chromosomes from a wild relative resulting in the generation of interspecific recombinant chromosomes. However, the ph1b mutant also enables recombination to occur between the homologous genomes of wheat, e.g. A/B, A/D, B/D, resulting in the generation of wheat intergenomic recombinant chromosomes. In this work we report on the presence of wheat intergenomic recombinants in the genomic background of hexaploid wheat/Amblyopyrum muticum introgression lines. The transfer of genomic rearrangements involving the D-genome through pentaploid crosses provides a strategy by which the D-genome of wheat can be introgressed into durum wheat. Hence, a pentaploid crossing strategy was used to transfer D-genome segments, introgressed with either the A- and/or the B-genome, into the tetraploid background of two durum wheat genotypes Karim and Om Rabi 5 in either the presence or absence of different Am. muticum (2n = 2x = 14, TT) introgressions. Introgressions were monitored in backcross generations to the durum wheat parents via multi-color genomic in situ hybridization (mc-GISH). Tetraploid lines carrying homozygous D-genome introgressions, as well as simultaneous homozygous D- and T-genome introgressions, were developed. Introgression lines were characterized via Kompetitive Allele-Specific PCR (KASP) markers and multi-color fluorescence in situ hybridization (FISH). Results showed that new wheat sub-genomic translocations were generated at each generation in progeny that carried any Am. muticum chromosome introgression irrespective of the linkage group that the segment was derived from. The highest frequencies of homologous recombination were observed between the A- and the D-genomes. Results indicated that the genotype Karim had a higher tolerance to genomic rearrangements and T-genome introgressions compared to Om Rabi 5. This indicates the importance of the selection of the parental genotype when attempting to transfer/develop introgressions into durum wheat from pentaploid crosses.

Genetic Analysis and Transfer of Favorable Exotic QTL Alleles for Grain Yield Across D Genome Using Two Advanced Backcross Wheat Populations

Hexaploid wheat evolved through a spontaneous hybridization of tetraploid wheat (Triticum turgidum, AABB) with diploid wild grass (Aegilops tauschii, DD). Recent genome sequencing found alarmingly low genetic diversity and abundance of repeated sequences across D genome as compared to AB genomes. This characteristic feature of D genome often results in a low recombination rate and abrupt changes in chromosome, which are the major hurdles to utilize the genetic potential of D genome in wheat breeding. In the present study, we evaluated two advanced backcross populations designated as B22 (250 BC2F3:6 lines) and Z86 (150 BC2F3:6 lines) to test their yield potential and to enrich the D genome diversity simultaneously. The populations B22 and Z86 were derived by crossing winter wheat cultivars Batis and Zentos with synthetic hexaploid wheat accessions Syn022L and Syn086L, respectively. These populations were genotyped using SNP markers and phenotyped for yield traits in ten environments in Germany. Marker analysis identified lower recombination rate across D genome as compared to A and B genomes in both populations. Further, we compared the genotype data with the trait grain yield to identify favorable exotic introgressions from synthetic wheat accessions. QTL analysis identified seven and 13 favorable exotic QTL alleles associated with enhancement or at least stable grain yield in populations B22 and Z86, respectively. These favorable introgressions were located on all chromosomes from 1D to 7D. The strongest exotic QTL allele on chromosome 1D at SNP marker RAC875_c51493_471 resulted in a relative increase of 8.6% in grain yield as compared to cultivated allele. The identified exotic introgressions will help to refine useful exotic chromosome segments for their incorporation for improving yield and increasing D genome diversity among cultivated varieties.

An Update of Recent Use of Aegilops Species in Wheat Breeding

Aegilops species have significantly contributed to wheat breeding despite the difficulties involved in the handling of wild species, such as crossability and incompatibility. A number of biotic resistance genes have been identified and incorporated into wheat varieties from Aegilops species, and this genus is also contributing toward improvement of complex traits such as yield and abiotic tolerance for drought and heat. The D genome diploid species of Aegilops tauschii has been utilized most often in wheat breeding programs. Other Aegilops species are more difficult to utilize in the breeding because of lower meiotic recombination frequencies; generally they can be utilized only after extensive and time-consuming procedures in the form of translocation/introgression lines. After the emergence of Ug99 stem rust and wheat blast threats, Aegilops species gathered more attention as a form of new resistance sources. This article aims to update recent progress on Aegilops species, as well as to cover new topics around their use in wheat breeding.

Genomic Analysis Confirms Population Structure and Identifies Inter-Lineage Hybrids in Aegilops tauschii

Aegilops tauschii, the D-genome donor of bread wheat, Triticum aestivum, is a storehouse of genetic diversity, and an important resource for future wheat improvement. Genomic and population analysis of 549 Ae. tauschii and 103 wheat accessions was performed by using 13,135 high quality SNPs. Population structure, principal component, and cluster analysis confirmed the differentiation of Ae. tauschii into two lineages; lineage 1 (L1) and lineage 2 (L2), the latter being the wheat D-genome donor. Lineage L1 contributes only 2.7% of the total introgression from Ae. tauschii for a set of United States winter wheat lines, confirming the great amount of untapped genetic diversity in L1. Lineage L2 accessions had overall greater allelic diversity and wheat accessions had the least allelic diversity. Both lineages also showed intra-lineage differentiation with L1 being driven by longitudinal gradient and L2 differentiated by altitude. There has previously been little reported on natural hybridization between L1 and L2. We found nine putative inter-lineage hybrids in the population structure analysis, each containing numerous lineage-specific private alleles from both lineages. One hybrid was confirmed as a recombinant inbred between the two lineages, likely artificially post collection. Of the remaining eight putative hybrids, a group of seven from Georgia carry 713 SNPs with private alleles, which points to the possibility of a novel L1-L2 hybrid lineage. To facilitate the use of Ae. tauschii in wheat improvement, a MiniCore consisting of 29 L1 and 11 L2 accessions, has been developed based on genotypic, phenotypic and geographical data. MiniCore reduces the collection size by over 10-fold and captures 84% of the total allelic diversity in the whole collection.

The Capacity to Buffer and Sustain Imbalanced D-Subgenome Chromosomes by the BBAA Component of Hexaploid Wheat Is an Evolved Dominant Trait

Successful generation of pentaploid wheat (genome, BBAAD) via interspecific hybridization between tetraploid wheat (BBAA) and hexaploid wheat (BBAADD) holds great promise to mutually exchange desirable traits between the two cultivated wheat species, as well as providing a novel facet for evolutionary studies of polyploid wheat. Taking advantage of the viable and fertile nature of an extracted tetraploid wheat (ETW) with a BBAA genome that is virtually identical with the BBAA component of a hexaploid common wheat, and a synthetic hexaploid wheat, we constructed four pentaploid wheats with several distinct yet complementary features, of which harboring homozygous BBAA subgenomes is a common feature. By using a combined FISH/GISH method that enables diagnosing all individual wheat chromosomes, we precisely karyotyped a larger number of cohorts from the immediate progenies of each of the four pentaploid wheats. We found that the BBAA component of hexaploid common wheat possesses a significantly stronger capacity to buffer and sustain imbalanced D genome chromosomes and appears to harbor more structural chromosome variations than the BBAA genome of tetraploid wheat. We also document that this stronger capacity of the hexaploid BBAA subgenomes behaves as a genetically controlled dominant trait. Our findings bear implications to the known greater than expected level of genetic diversity in, and the remarkable adaptability of, hexaploid common wheat as a staple crop of global significance, as well as in using pentaploidy as intermediates for reciprocal introgression of useful traits between tetraploid and hexaploid wheat cultivars.

Introgression of the Aegilops speltoides Su1-Ph1 Suppressor into Wheat

Meiotic pairing between homoeologous chromosomes in polyploid wheat is inhibited by the Ph1 locus on the long arm of chromosome 5 in the B genome. Aegilops speltoides (genomes SS), the closest relative of the progenitor of the wheat B genome, is polymorphic for genetic suppression of Ph1. Using this polymorphism, two major suppressor loci, Su1-Ph1 and Su2-Ph1, have been mapped in Ae. speltoides. Su1-Ph1 is located in the distal, high-recombination region of the long arm of the Ae. speltoides chromosome 3S. Its location and tight linkage to marker Xpsr1205-3S makes Su1-Ph1 a suitable target for introgression into wheat. Here, Xpsr1205-3S was introgressed into hexaploid bread wheat cv. Chinese Spring (CS) and from there into tetraploid durum wheat cv. Langdon (LDN). Sequential fluorescence in situ hybridization and genomic in situ hybridization showed that an Ae. speltoides segment with Xpsr1205-3S replaced the distal end of the long arm of chromosome 3A. In the CS genetic background, the chromosome induced homoeologous chromosome pairing in interspecific hybrids with Ae. peregrina but not in progenies from crosses involving alien disomic substitution lines. In the LDN genetic background, the chromosome induced homoeologous chromosome pairing in both interspecific hybrids and progenies from crosses involving alien disomic substitution lines. We conclude that the recombined chromosome harbors Su1-Ph1 but its expression requires expression of complementary gene that is present in LDN but absent in CS. We suggest that it is unlikely that Su1-Ph1 and ZIP4-1, a paralog of Ph1 located on wheat chromosomes 3A and 3B and Ae. tauschii chromosome 3D, are equivalent. The utility of Su1-Ph1 for induction of recombination between homoeologous chromosomes in wheat is illustrated.