Construction of a hexaploid wheat (Triticum aestivum L.) bacterial artificial chromosome library for cloning genes for stripe rust resistance

Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance

KEY MESSAGE

Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance. Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the Puccinia fungus, responsible for rust diseases, evolve frequently and globally.

Construction and characterization of a bacterial artificial chromosome library for Gossypium mustelinum

A bacterial artificial chromosome (BAC) library for G. mustelinum Miers ex G. Watt (AD₄) was constructed. Intact nuclei from G. mustelinum (AD₄) were used to isolate high molecular weight DNA, which was partially cleaved with Hind III and cloned into pSMART BAC (Hind III) vectors. The BAC library consisted of 208,182 clones arrayed in 542 384-microtiter plates, with an average insert size of 121.72 kb ranging from 100 to 150 kb. About 2% of the clones did not contain inserts. Based on an estimated genome size of 2372 Mb for G. mustelinum, the BAC library was estimated to have a total coverage of 10.50 × genome equivalents. The high capacity library of G. mustelinum will serve as a giant gene resource for map-based cloning of quantitative trait loci or genes associated with important agronomic traits or resistance to Verticillium wilt, physical mapping and comparative genome analysis.

Construction and characterization of three wheat bacterial artificial chromosome libraries

We have constructed three bacterial artificial chromosome (BAC) libraries of wheat cultivar Triticum aestivum Wangshuibai, germplasms T. monococcum TA2026 and TA2033. A total of 1,233,792,170,880 and 263,040 clones were picked and arrayed in 384-well plates. On the basis of genome sizes of 16.8 Gb for hexaploid wheat and 5.6 Gb for diploid wheat, the three libraries represented 9.05-, 2.60-, and 3.71-fold coverage of the haploid genomes, respectively. An improved descending pooling system for BAC libraries screening was established. This improved strategy can save 80% of the time and 68% of polymerase chain reaction (PCR) with the same successful rate as the universal 6D pooling strategy.

Construction and characterization of a bacterial artificial chromosome library for the hexaploid wheat line 92R137

For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from the HindIII digestion and 375,552 from the BamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from the HindIII sublibrary and 573 clones from the BamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, the HindIII sublibrary was estimated to have a 3.01-fold coverage and the BamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as gene Yr26 for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools with Xwe173, a marker tightly linked to Yr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning of Yr26 and other genes of interest.

BAC libraries from wheat chromosome 7D: efficient tool for positional cloning of aphid resistance genes

Positional cloning in bread wheat is a tedious task due to its huge genome size and hexaploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which makes their screening very laborious. Here, we present a targeted approach based on chromosome-specific BAC libraries. Such libraries were constructed from flow-sorted arms of wheat chromosome 7D. A library from the short arm (7DS) consisting of 49,152 clones with 113 kb insert size represented 12.1 arm equivalents whereas a library from the long arm (7DL) comprised 50,304 clones of 116 kb providing 14.9x arm coverage. The 7DS library was PCR screened with markers linked to Russian wheat aphid resistance gene DnCI2401, the 7DL library was screened by hybridization with a probe linked to greenbug resistance gene Gb3. The small number of clones combined with high coverage made the screening highly efficient and cost effective.

Constructing Physical and Genomic Maps for Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen, by Comparing Its EST Sequences to the Genomic Sequence of P. graminis f. sp. tritici, the Wheat Stem Rust Pathogen

The wheat stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst), does not have a known alternate host for sexual reproduction, which makes it impossible to study gene linkages through classic genetic and molecular mapping approaches. In this study, we compared 4,219 Pst expression sequence tags (ESTs) to the genomic sequence of P. graminis f. sp. tritici (Pgt), the wheat stem rust fungus, using BLAST searches. The percentages of homologous genes varied greatly among different Pst libraries with 54.51%, 51.21%, and 13.61% for the urediniospore, germinated urediniospore, and haustorial libraries, respectively, with an average of 33.92%. The 1,432 Pst genes with significant homology with Pgt sequences were grouped into physical groups corresponding to 237 Pgt supercontigs. The physical relationship was demonstrated by 12 pairs (57%), out of 21 selected Pst gene pairs, through PCR screening of a Pst BAC library. The results indicate that the Pgt genome sequence is useful in constructing Pst physical maps.

Molecular mapping of a stripe rust resistance gene in spring wheat cultivar Zak

Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici, is one of the most devastating foliar diseases of wheat (Triticum aestivum) worldwide. Growing resistant cultivars is the best approach for control of the disease. Although the stripe rust resistance in spring wheat cv. Zak has been circumvented by a group of races of the pathogen predominant in the United States since 2000, the resistance genes in Zak were unknown. To identify and map the genes for resistance to stripe rust, Zak was crossed with susceptible wheat genotype 'Avocet Susceptible'. Seedlings of the parents and F1, F2, and F3 progeny were tested with P. striiformis f. sp. tritici races PST-43 and PST-45 under controlled greenhouse conditions. Genetic analysis determined that Zak has a single dominant gene, designated as YrZak, conferring race-specific all-stage resistance. Resistance gene analog polymorphism (RGAP), simple sequence repeat (SSR), and sequence-tagged site (STS) techniques were used to identify molecular markers linked to YrZak. A linkage group of three RGAP, three SSR, and three STS markers was constructed for YrZak using 205 F3 lines. Amplification of the complete set of Chinese Spring nulli-tetrasomic lines with RGAP marker Xwgp102 indicated that YrZak is present on chromosome 2B. The three SSR markers further mapped YrZak to the long arm of chromosome 2B. Amplification of chromosome 2B deletion lines with SSR marker Xgwm501 further confirmed that YrZak is on chromosome 2BL. To determine the genetic distance between YrZak and Yr5, which also is present on chromosome 2BL, 300 F2 plants from cross Zak/Yr5 were tested with PST-43. Six susceptible plants were identified from the F2 population, indicating that YrZak and Yr5 are approximately 42 centimorgans apart. The results of race reactions and chromosomal locations indicated that YrZak is different from previously identified genes for resistance to stripe rust. This gene should be useful in monitoring virulence changes in the pathogen population and in studying host-pathogen interactions.

Physical analysis of the complex rye (Secale cereale L.) Alt4 aluminium (aluminum) tolerance locus using a whole-genome BAC library of rye cv. Blanco

Rye is a diploid crop species with many outstanding qualities, and is important as a source of new traits for wheat and triticale improvement. Rye is highly tolerant of aluminum (Al) toxicity, and possesses a complex structure at the Alt4 Al tolerance locus not found at the corresponding locus in wheat. Here we describe a BAC library of rye cv. Blanco, representing a valuable resource for rye molecular genetic studies, and assess the library's suitability for investigating Al tolerance genes. The library provides 6 x genome coverage of the 8.1 Gb rye genome, has an average insert size of 131 kb, and contains only ~2% of empty or organelle-derived clones. Genetic analysis attributed the Al tolerance of Blanco to the Alt4 locus on the short arm of chromosome 7R, and revealed the presence of multiple allelic variants (haplotypes) of the Alt4 locus in the BAC library. BAC clones containing ALMT1 gene clusters from several Alt4 haplotypes were identified, and will provide useful starting points for exploring the basis for the structural variability and functional specialization of ALMT1 genes at this locus.

Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The 55 K Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC(7):F(4)) that differ for the Yr5 stripe rust resistance locus, with the objective of developing genetic markers linked to Yr5. Ninety-one probe sets showing ELPs and 118 SFP-containing probe sets were identified between isolines, of which just nine ELP probe sets also contained SFPs. The proportion of the transcriptome estimated to be variable between isolines from this analysis was 0.30% for the ELPs and 0.39% for the SFPs, which was highly similar to the theoretical genome difference between isolines of ~0.39%. Using wheat-rice synteny, both ELPs and SFPs mainly clustered on long arms of rice chromosomes four and seven, which are syntenous to wheat chromosomes 2L (Yr5 locus) and 2S, respectively. The strong physical correlation between the two types of polymorphism indicated that the ELPs may be regulated by cis-acting DNA polymorphisms. Twenty SFPs homologous to rice 4L were used to develop additional genetic markers for Yr5. Physical mapping of the probe sets containing SFPs to wheat chromosomes identified nine on the target chromosome 2BL, thus wheat-rice synteny greatly enhanced the selection of SFPs that were located on the desired wheat chromosome. Of these nine, four were converted into polymorphic cleaved amplified polymorphic sequence (CAPS) markers between Yr5 and yr5 isolines, and one was mapped within 5.3 cM of the Yr5 locus. This study represents the first array-based polymorphism survey in near-isogenic genotypes, and the results are applied to an agriculturally important trait.