Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium).

Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.

Uncovering the Genetic Architecture of Seed Weight and Size in Intermediate Wheatgrass through Linkage and Association Mapping.

Intermediate wheatgrass [IWG; (Host) Barkworth & D.R. Dewey subsp. ] is being developed as a new perennial grain crop that has a large allohexaploid genome similar to that of wheat ( L.). Breeding for increased seed weight is one of the primary goals for improving grain yield of IWG. As a new crop, however, the genetic architecture of seed weight and size has not been characterized, and selective breeding of IWG may be more intricate than wheat because of its self-incompatible mating system and perennial growth habit. Here, seed weight, seed area size, seed width, and seed length were evaluated across multiple years, in a heterogeneous breeding population comprised of 1126 genets and two clonally replicated biparental populations comprised of 172 and 265 genets. Among 10,171 DNA markers discovered using genotyping-by-sequencing (GBS) in the breeding population, 4731 markers were present in a consensus genetic map previously constructed using seven full-sib populations. Thirty-three quantitative trait loci (QTL) associated with seed weight and size were identified using association mapping (AM), of which 23 were verified using linkage mapping in the biparental populations. About 37.6% of seed weight variation in the breeding population was explained by 15 QTL, 12 of which also contributed to either seed length or seed width. When performing either phenotypic selection or genomic selection for seed weight, we observed the frequency of favorable QTL alleles were increased to >46%. Thus, by combining AM and genomic selection, we can effectively select the favorable QTL alleles for seed weight and size in IWG breeding populations.

Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing.

KEY MESSAGE: Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding. Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop and is actively being improved by several breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and genetic marker reference maps are needed. We present here the first consensus genetic map for intermediate wheatgrass (IWG), which confirms the species' allohexaploid nature (2n = 6x = 42) and homology to Triticeae genomes. Genotyping-by-sequencing was used to identify markers that fit expected segregation ratios and construct genetic maps for 13 heterogeneous parents of seven full-sib families. These maps were then integrated using a linear programming method to produce a consensus map with 21 linkage groups containing 10,029 markers, 3601 of which were present in at least two populations. Each of the 21 linkage groups contained between 237 and 683 markers, cumulatively covering 5061 cM (2891 cM--Kosambi) with an average distance of 0.5 cM between each pair of markers. Through mapping the sequence tags to the diploid (2n = 2x = 14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. The consensus map is a valuable tool for wheat breeders to map important disease-resistance genes within intermediate wheatgrass. These genomic tools can help lead to rapid improvement of IWG and development of high-yielding cultivars of this perennial grain that would facilitate the sustainable intensification of agricultural systems.

Establishment and Optimization of Genomic Selection to Accelerate the Domestication and Improvement of Intermediate Wheatgrass.

Intermediate wheatgrass (IWG) is a perennial species and has edible and nutritious grain and desirable agronomic traits, including large seed size, high grain yield, and biomass. It also has the potential to provide ecosystem services and an economic return to farmers. However, because of its allohexaploidy and self-incompatibility, developing molecular markers for genetic analysis and molecular breeding has been challenging. In the present study, using genotyping-by-sequencing (GBS) technology, 3436 genome-wide markers discovered in a biparental population with 178 genets, were mapped to 21 linkage groups (LG) corresponding to 21 chromosomes of IWG. Genomic prediction models were developed using 3883 markers discovered in a breeding population containing 1126 representative genets from 58 half-sib families. High predictive ability was observed for seven agronomic traits using cross-validation, ranging from 0.46 for biomass to 0.67 for seed weight. Optimization results indicated that 8 to 10 genets from each half-sib family can form a good training population to predict the breeding value of their siblings, and 1600 genome-wide markers are adequate to capture the genetic variation in the current breeding population for genomic selection. Thus, with the advances in sequencing-based marker technologies, it was practical to perform molecular genetic analysis and molecular breeding on a new and challenging species like IWG, and genomic selection could increase the efficiency of recurrent selection and accelerate the domestication and improvement of IWG.