By physically mapping 3025 loci including 252 phenotypically characterized genes and 17 quantitative trait loci (QTLs) relative to 334 deletion breakpoints, we localized the gene-containing fraction to 29% of the wheat genome present as 18 major and 30 minor gene-rich regions (GRRs). The GRRs varied both in gene number and density. The five largest GRRs physically spanning <3% of the genome contained 26% of the wheat genes. Approximate size of the GRRs ranged from 3 to 71 Mb. Recombination mainly occurred in the GRRs. Various GRRs varied as much as 128-fold for gene density and 140-fold for recombination rates. Except for a general suppression in 25–40% of the chromosomal region around centromeres, no correlation of recombination was observed with the gene density, the size, or chromosomal location of GRRs. More than 30% of the wheat genes are in recombination-poor regions thus are inaccessible to map-based cloning.

Significance: Maintaining diploid-like pairing behavior is essential for a polyploid to establish as a new species. The Pairing homeologous 1 ( Ph1 ) gene, regulating such behavior in polyploid wheat, was identified in 1958, but its molecular function remained elusive. The present communication reports identification of the candidate Ph1 ( C-Ph1 ) gene that is expressed exclusively during meiotic metaphase I, whose silencing resulted in formation of multivalents like the Ph1 gene mutations. Although the C-Ph1 gene has three homoeologous copies, the 5B copy has diverged in sequence from the other two copies. Heterologous gene silencing of the Arabidopsis homologue of the C-Ph1 gene also confirmed its function. Molecular characterization of this gene will make it possible to develop precise alien introgression strategies.

A marker-assisted background selection (MABS)-based gene introgression approach in wheat (Triticum aestivum L.) was optimized, where 97% or more of a recurrent parent genome (RPG) can be recovered in just two backcross (BC) generations. A four-step MABS method was developed based on ‘Plabsim’ computer simulations and wheat genome structure information. During empirical optimization of this method, double recombinants around the target gene were selected in a step-wise fashion during the two BC cycles followed by selection for recurrent parent genotype on non-carrier chromosomes. The average spacing between carrier chromosome markers was <4 cM. For non-carrier chromosome markers that flanked each of the 48 wheat gene-rich regions, this distance was ∼12 cM. Employed to introgress seedling stripe rust (Puccinia striiformis f. sp. tritici) resistance gene Yr15 into the spring wheat cultivar ‘Zak’, marker analysis of 2,187 backcross-derived progeny resulted in the recovery of a BC₂F_2∶3 plant with 97% of the recurrent parent genome. In contrast, only 82% of the recurrent parent genome was recovered in phenotypically selected BC₄F₇ plants developed without MABS. Field evaluation results from 17 locations indicated that the MABS-derived line was either equal or superior to the recurrent parent for the tested agronomic characteristics. Based on these results, MABS is recommended as a strategy for rapidly introgressing a targeted gene into a wheat genotype in just two backcross generations while recovering 97% or more of the recurrent parent genotype.

The objectives of this study were to isolate and physically localize expressed resistance (R) genes on wheat chromosomes. Irrespective of the host or pest type, most of the 46 cloned R genes from 12 plant species share a strong sequence similarity, especially for protein domains and motifs. By utilizing this structural similarity to perform modified RNA fingerprinting and data mining, we identified 184 putative expressed R genes of wheat. These include 87 NB/LRR types, 16 receptor-like kinases, and 13 Pto-like kinases. The remaining were seven Hm1 and two Hs1^pro-1 homologs, 17 pathogenicity related, and 42 unique NB/kinases. About 76% of the expressed R-gene candidates were rare transcripts, including 42 novel sequences. Physical mapping of 121 candidate R-gene sequences using 339 deletion lines localized 310 loci to 26 chromosomal regions encompassing ∼16% of the wheat genome. Five major R-gene clusters that spanned only ∼3% of the wheat genome but contained ∼47% of the candidate R genes were observed. Comparative mapping localized 91% (82 of 90) of the phenotypically characterized R genes to 18 regions where 118 of the R-gene sequences mapped.

Successful stand establishment is prerequisite for optimum crop yields. In some low-precipitation zones, wheat (Triticum aestivum L.) is planted as deep as 200 mm below the soil surface to reach adequate soil moisture for germination. To better understand the relationship of coleoptile length and other seed characteristics with emergence from deep planting (EDP), we evaluated 662 wheat cultivars grown around the world since the beginning of the 20^th century. Coleoptile length of collection entries ranged from 34 to 114 mm. A specialized field EDP test showed dramatic emergence differences among cultivars ranging from 0–66% by 21 days after planting (DAP). Less than 1% of entries had any seedlings emerged by 7 DAP and 43% on day 8. A wide range of EDP within each coleoptile length class suggests the involvement of genes other than those controlling coleoptile length. Emergence was correlated with coleoptile length, but some lines with short coleoptiles ranked among the top emergers. Coleoptiles longer than 90 mm showed no advantage for EDP and may even have a negative effect. Overall, coleoptile length accounted for only 28% of the variability in emergence among entries; much lower than the 60% or greater reported in previous studies. Seed weight had little correlation with EDP. Results show that EDP is largely controlled by yet poorly understood mechanisms other than coleoptile length.