A High-Resolution Map of Wheat QYr.ucw-1BL, an Adult Plant Stripe Rust Resistance Locus in the Same Chromosomal Region as Yr29

The appearance of highly virulent and more aggressive races of f. sp. () during the last two decades has led to stripe rust epidemics worldwide and to the rapid erosion of effective resistance genes. In this study, we mapped an adult-plant resistance locus from the Argentinean wheat ( L.) cultivar Klein Chajá, which is effective against these new races. By using wheat exome capture data and a large population of 2480 segregating plants (4960 gametes), we mapped within a 0.24-cM region [332 kb in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0] on chromosome arm 1BL. This region overlaps with current maps of the adult-plant resistance gene , which has remained effective for more than 60 yr. An allelism test failed to find recombination between and and yielded similar resistance phenotypes for the two loci. These results, together with similar haplotypes in the candidate region, suggested that and might represent the same gene. However, we cannot rule out the possibility of tightly linked but different genes because most of the 13 genes in the candidate region are annotated with functions associated with disease resistance. To evaluate their potential as candidate genes, we characterized their polymorphisms between resistant and susceptible haplotypes. Finally, we used these polymorphisms to develop high-throughput markers to accelerate the deployment of these resistance loci in wheat breeding programs.

Molecular Mapping of Fusarium Head Blight Resistance in the Spring Wheat Line ND2710

ND2710 is a hard red spring wheat line with a very high level of resistance to Fusarium head blight (FHB). It was selected from the progeny of a cross between ND2603 (an advanced breeding line derived from the Sumai 3/Wheaton cross) and Grandin (a spring wheat cultivar). The FHB resistance of ND2710 is presumably derived from Sumai 3 because the other parents (Grandin and Wheaton) are very susceptible to FHB. To identify and map the quantitative trait loci (QTL) for FHB resistance in ND2710, we developed a mapping population consisting of 233 recombinant inbred lines (RILs) from the cross between ND2710 and the spring wheat cultivar Bobwhite. These RILs along with their parents and checks were evaluated for reactions to FHB in three greenhouse experiments and one field experiment during 2013 to 2014. The population was also genotyped with the wheat 90K iSelect single-nucleotide polymorphism (SNP) assay, and a genetic linkage map was developed with 1,373 non-cosegregating SNP markers, which were distributed on all 21 wheat chromosomes spanning 914.98 centimorgans of genetic distance. Genetic analyses using both phenotypic and genotypic data identified one major QTL (Qfhb.ndwp-3B) on the short arm of chromosome 3B, and three minor QTL (Qfhb.ndwp-6B, Qfhb.ndwp-2A, and Qfhb.ndwp-6A) on 6B, 2A, and 6A, respectively. The major QTL on 3B was detected in all experiments and explained 5 to 20% of the phenotypic variation, while the three minor QTL on 6B, 2A, and 6A explained 5 to 12% phenotypic variation in at least two experiments, except for Qfhb.ndwp-2A, which was only detected in the field experiment. Qfhb.ndwp-3B and Qfhb.ndwp-6B were mapped to the genomic regions containing Fhb1 and Fhb2, respectively, confirming that they originated from Sumai 3. The additive effect of the major and minor QTL may contribute to the high level of FHB resistance in ND2710. The SNP markers closely linked to the FHB resistance QTL will be useful for marker-assisted selection of FHB resistance in wheat breeding programs.

Development of molecular markers for genetic male sterility in Gossypium hirsutum

Genetic male sterility (GMS) in cotton mediated by two homozygous recessive genes, ms5ms5 and ms6ms6, is expressed as non-dehiscent anthers and unviable pollen grains. Sequence analysis on ms5 and ms6 loci in Gossypium hirsutum was conducted to reveal genomic variation at these two loci between GMS and wild-type G. hirsutum inbred lines, and sequence polymorphism linked to ms5 on A12 and ms6 on D12 was revealed. A haplotype marker set that consisted of four SNPs targeting both ms5 and ms6 gene regions was developed and validated for association with GMS in cotton. Predictability of GMS phenotype by this haplotype SNP set was over 99 %. GMS haplotype marker set can serve as a high-throughput molecular breeding tool to select GMS individuals and improve hybrid production efficiency.

Insular organization of gene space in grass genomes

Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands “gene insulae” to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.

Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes

Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated sequence content in a genome, we suggest that the amount and activity of repeated sequences are important factors determining the number of genes in a genome.

RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development

Transposable elements (TE) exist in the genomes of nearly all eukaryotes. TE mobilization through ‘cut-and-paste’ or ‘copy-and-paste’ mechanisms causes their insertions into other repetitive sequences, gene loci and other DNA. An insertion of a TE commonly creates a unique TE junction in the genome. TE junctions are also randomly distributed along chromosomes and therefore useful for genome-wide marker development. Several TE-based marker systems have been developed and applied to genetic diversity assays, and to genetic and physical mapping. A software tool ‘RJPrimers’ reported here allows for accurate identification of unique repeat junctions using BLASTN against annotated repeat databases and a repeat junction finding algorithm, and then for fully automated high-throughput repeat junction-based primer design using Primer3 and BatchPrimer3. The software was tested using the rice genome and genomic sequences of Aegilops tauschii. Over 90% of repeat junction primers designed by RJPrimers were unique. At least one RJM marker per 10 Kb sequence of A. tauschii was expected with an estimate of over 0.45 million such markers in a genome of 4.02 Gb, providing an almost unlimited source of molecular markers for mapping large and complex genomes. A web-based server and a command line-based pipeline for RJPrimers are both available at http://wheat.pw.usda.gov/demos/RJPrimers/.

Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.

Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins

The wheat high molecular weight (HMW) glutenins are important seed storage proteins that determine bread-making quality in hexaploid wheat (Triticum aestivum). In this study, detailed comparative sequence analyses of large orthologous HMW glutenin genomic regions from eight grass species, representing a wide evolutionary history of grass genomes, reveal a number of lineage-specific sequence changes. These lineage-specific changes, which resulted in duplications, insertions, and deletions of genes, are the major forces disrupting gene colinearity among grass genomes. Our results indicate that the presence of the HMW glutenin gene in Triticeae genomes was caused by lineage-specific duplication of a globulin gene. This tandem duplication event is shared by Brachypodium and Triticeae genomes, but is absent in rice, maize, and sorghum, suggesting the duplication occurred after Brachypodium and Triticeae genomes diverged from the other grasses ~35 Ma ago. Aside from their physical location in tandem, the sequence similarity, expression pattern, and conserved cis-acting elements responsible for endosperm-specific expression further support the paralogous relationship between the HMW glutenin and globulin genes. While the duplicated copy in Brachypodium has apparently become nonfunctional, the duplicated copy in wheat has evolved to become the HMW glutenin gene by gaining a central prolamin repetitive domain.

Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.

Complementation of the pina (null) allele with the wild type Pina sequence restores a soft phenotype in transgenic wheat

The tightly linked puroindoline genes, Pina and Pinb, control grain texture in wheat, with wild type forms of both giving soft, and a sequence alteration affecting protein expression or function in either giving rise to hard wheat. Previous experiments have shown that addition of wild type Pina in the presence of mutated Pinb gave intermediate grain texture but addition of wild type Pinb gave soft grain. This raises questions as to whether Pina may be less functional than Pinb. Our goal here was to develop and characterize wheat lines expressing the wild type Pina-D1a sequence in hard wheat with the null mutation (Pina-D1b) for Pina. Three transgenic lines plus Bobwhite were evaluated in two environments. Grain texture, grain protein, and kernel weight were determined for the transgenic lines and Bobwhite. The three transgenic lines had soft phenotype, and none of the transgenic lines differed from Bobwhite for grain protein or kernel weight. The soft phenotype was accompanied by increases in Pina transcript accumulation. Total Triton X-114 extractable PINA and PINB increased from 2.5 to 5.5 times those from a soft wheat reference sample, and friabilin, PINA and PINB bound to starch, increased from 3.8 to 7.8 times those of the soft wheat reference. Bobwhite showed no starch bound PINA, but transgenic lines had levels from 5.3 to 13.7 times those of the soft wheat reference sample. Starch bound PINB in transgenic lines also increased from 0.9 to 2.5 times that for the soft wheat reference sample. The transgenic expression of wild type Pina sequence in the Pina null genotype gave soft grain with the characteristics of soft wheat including increased starch bound friabilin. The results support the hypothesis that both wild type Pin genes need to be present for friabilin formation and soft grain.