Key message The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. Abstract The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, ‘Jagger’ and ‘CDC Stanley,’ and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.

16Wild relatives of hexaploid wheat (Triticum aestivum) are the reservoirs of novel allelic 17 diversity with great potential to improve many agronomic traits in wheat. Here, we 18 investigated the genome-wide patterns and efficiency of Aegilops tauschii allele introgression 19 into the winter wheat cultivars. The introgression population of 351 BC 1 F 3 : 5 lines was 20 selected based on phenology and development characteristics from crosses between six 21 hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. Complexity reduced genomic 22 library sequencing was used to develop SNP markers and infer the regions of identity-by-23 descent and the boundaries of the introgressed segments. Using a diverse panel of 116 Ae. 24 tauschii accessions, it was possible to infer that introgression lines had single or multiple IBD 25 segments from accessions of diverse geographic origin. Introgression frequency was high at 26 the ends of chromosomes and low in the large pericentromeric 2/3 of the chromosome arms 27 characterized by low crossover rate. While the effect of selection for free-threshing genotypes 28 was evident around the domestication gene Tg, reduction in the frequency of introgression 29 was limited to relatively small regions flanking the gene. These results suggest that the 30 effects of phenotypic selection on the introgressed wild relative's alleles at the early 31 generations of population development are strongly influenced by the distribution of 32 crossover frequency across genome, consistent with the Hill-Robertson effect. Our study 33 offers insights into the introgression population development to ensure retention of genetic 34 2 diversity across entire genome and presents a resource that will be valuable for deploying 35 wild relative diversity in breeding programs to create climate resilient and disease resistant 36 varieties with improved yield and quality traits. 37 38Introduction 39Wheat production is constrained by several biotic and abiotic factors, yet the demand 40 for wheat is expected to double by 2050. A yield increase of ~2.4 % per year has been 41 projected as required to close the gap between the current production level and an increasing 42 demand (Ray et al. 2013). While this goal can be achieved by improving agronomic 43 practices, expanding the production area and/or deployment of high-yielding wheat varieties, 44 the first two alternatives are unsustainable because land is a limited resource and most 45 effective agronomic practices are costly. Accelerated wheat improvement through extensive 46 deployment of available genomics tools and genetic resources, including close and distant 47 wild relatives of wheat, is viewed as the most effective and sustainable alternative to 48 increasing yield. 49Allohexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD) resulted from 50 hybridization of Triticum turgidum (2n = 4x = 28, AABB) and Aegilops tauschii ssp. 51 strangulata (2n = 2x = 14, DD) (Kihara 1944; Luo et al. 2007;Wang et al. 2013). 52 Domestication of wheat followed by con...

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.

No abstract

Fusarium head blight (FHB) is a disease of small grains most commonly associated with the fungal pathogen Fusarium graminearum. Development and deployment of resistant cultivars has proved to be an effective method to combat the disease; however, the majority of major resistance has historically been found in exotic material. Transferring resistance from these sources into locally adapted cultivars has been a slow process due to linkage drag. Therefore, it is important for breeders to search for sources of resistance in native material. This study was conducted to identify quantitative trait loci (QTL) for resistance to spread of FHB within the spike (Type II resistance), accumulation of deoxynivalenol toxin in grain (Type III resistance), and resistance to kernel infection (Type IV resistance) using a doubled‐haploid population developed from a cross between the hard red winter wheat (Triticum aestivum L.) cultivars Art and Everest. Four QTL conferring resistance to FHB traits were detected on chromosomes 2D, 4B, and 4D. Qfhb.ksu‐2D, located on the short arm of 2D, is located near the major photoperiod gene Ppd‐D1 and was associated with all three FHB traits. Qfhb.ksu‐2D.1 is on the long arm of 2D and was associated with percentage symptomatic spikelets (PSS). The QTL on chromosomes 4B and 4D were associated with PSS and overlapped with the major height genes Rht‐B1 and Rht‐D1, respectively. In this study, the haplotype analysis for Ppd‐D1 showed significant associations between the photoperiod‐sensitive allele Ppd‐D1b and lower levels of all three FHB traits. The haplotype analysis for the Rht‐B1 and Rht‐D1 loci showed significant associations between the dwarfing alleles and increased resistance to PSS.