Implementing multi-trait genomic selection to improve grain milling quality in oats (Avena sativa L.).

Oats (Avena sativa L.) provide unique nutritional benefits and contribute to sustainable agricultural systems. Breeding high-value oat varieties that meet milling industry standards is crucial for satisfying the demand for oat-based food products. Test weight, thins, and groat percentage are primary traits that define oat milling quality and the final price of food-grade oats. Conventional selection for milling quality is costly and burdensome. Multi-trait genomic selection (MTGS) combines information from genome-wide markers and secondary traits genetically correlated with primary traits to predict breeding values of primary traits on candidate breeding lines. MTGS can improve prediction accuracy and significantly accelerate the rate of genetic gain. In this study, we evaluated different MTGS models that used morphometric grain traits to improve prediction accuracy for primary grain quality traits within the constraints of a breeding program. We evaluated 558 breeding lines from the University of Illinois Oat Breeding Program across 2 years for primary milling traits, test weight, thins, and groat percentage, and secondary grain morphometric traits derived from kernel and groat images. Kernel morphometric traits were genetically correlated with test weight and thins percentage but were uncorrelated with groat percentage. For test weight and thins percentage, the MTGS model that included the kernel morphometric traits in both training and candidate sets outperformed single-trait models by 52% and 59%, respectively. In contrast, MTGS models for groat percentage were not significantly better than the single-trait model. We found that incorporating kernel morphometric traits can improve the genomic selection for test weight and thins percentage.

An online database for einkorn wheat to aid in gene discovery and functional genomics studies.

Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL  https://wheat.pw.usda.gov/GG3/pangenome.

Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat.

Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.

Einkorn genomics sheds light on history of the oldest domesticated wheat.

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits.

Einkorn wheat (Triticum monococcum) is an ancient grain crop and a close relative of the diploid progenitor (T. urartu) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars.

Primary Systemic Amyloidosis: A Case Report.

Primary systemic amyloidosis is a systemic disease characterised by the deposition of misfolded proteins extracellularly in different organs without any known cause in the background, eventually leading to multiorgan dysfunction and death. The incidence of primary amyloidosis is estimated at 5.1-12.8 cases per million, with a poor prognosis. We report a case of a 69-year male with lower back pain, shortness of breath, and anasarca diagnosed as primary systemic amyloidosis by serum-free light chain assay and kidney needle biopsy. He was started on intravenous bortezomib and dexamethasone. Though he adhered to his medications, with time he developed renal insufficiency marked by azotemia following which hemodialysis was performed. Primary systemic amyloidosis is a rare clinical condition with a very poor prognosis. Further studies are needed to understand the proper pathophysiology and treatment of the disease. Keywords: cardiomyopathies; case reports; primary amyloidosis.

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations.

The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T. aestivum x Hordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

Genetic characterization and curation of diploid A-genome wheat species.

A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.), and Triticum urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC) using genotyping by sequencing and identified 13,860 curated single-nucleotide polymorphisms. Genomic analysis detected misclassified and genetically identical (>99%) accessions, with most of the identical accessions originating from the same or nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were genetically identical, supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that T. urartu is the closest A-genome diploid to the A-subgenome in common wheat (Triticum aestivum L.) through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, ß, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring a domestication selection signature at the Non-brittle rachis 1 (Btr1) locus on the short arm of chromosome 3Am at ∼70 Mb. We established an A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 79% of allelic variants in the A-genome collection and constituted a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.

Mapping freezing tolerance QTL in alfalfa: based on indoor phenotyping.

BACKGROUND: Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were tested for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping-by-sequencing (GBS) and the quantitative trait loci (QTL) associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. RESULTS: Alfalfa FT screening method optimized in this experiment comprises three major steps: clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is a useful indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL associated with four traits; nine for visual rating-based FT, five for percentage survival (PS), four for treated to control regrowth ratio (RR), and two for treated to control biomass ratio (BR). Some QTL positions overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) were from the potential genic region for a cold tolerance gene CBF. The BLAST alignment of a CBF sequence of M. truncatula, a close relative of alfalfa, against the alfalfa reference showed that the gene's ortholog resides around 75 Mb on chromosome 6. CONCLUSIONS: The indoor freezing tolerance selection method reported is useful for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources for the research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.

Correction to: QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.).

In the article [1], in 'Methods' section and 'G x E and heritability' subsection, there is an error in the formula of heritability (H2).

QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.).

BACKGROUND: The genetic and genomic basis of flowering time and biomass yield in alfalfa (Medicago sativa L.) remains poorly understood mainly due to the autopolyploid nature of the species and the lack of adequate genomic resources. We constructed linkage maps using genotyping-by-sequencing (GBS) based single dose allele (SDA) SNP and mapped alfalfa timing of flowering (TOF), spring yield (SY), and cumulative summer biomass (CSB) in a pseudo-testcross F1 population derived from a fall dormant (3010) and a non-dormant (CW 1010) cultivars. We analyzed the quantitative trait loci (QTL) to identify conserved genomic regions and detected molecular markers and potential candidate genes associated with the traits to improve alfalfa and provide genomic resources for the future studies. RESULTS: This study showed that both fall dormant and non-dormant alfalfa cultivars harbored QTL for early and late flowering, suggesting that flowering time in alfalfa is not an indicator of its fall dormancy (FD) levels. A weak phenotypic correlation between the flowering time and fall dormancy (FD) in F1 and checks also corroborated that alfalfa FD and TOF are not the predictors of one another. The relationship between flowering time and alfalfa biomass yield was not strong, but the non-dormant had relatively more SY than dormant. Therefore, selecting superior alfalfa cultivars that are non-dormant, winter-hardy, and early flowering would allow for an early spring harvest with enhanced biomass. In this study, we found 25 QTL for TOF, 17 for SY and six QTL for CSB. Three TOF related QTL were stable and four TOF QTL were detected in the corresponding genomic locations of the flowering QTL of M. truncatula, an indication of possible evolutionarily conserved regions. The potential candidate genes for the SNP sequences of QTL regions were identified for all three traits and these genes would be potential targets for further molecular studies. CONCLUSIONS: This research showed that variation in alfalfa flowering time after spring green up has no association with dormancy levels. Here we reported QTL, markers, and potential candidate genes associated with spring flowering time and biomass yield of alfalfa, which constitute valuable genomic resources for improving these traits via marker-assisted selection (MAS).

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping.

Understanding key adaptation traits is crucial to developing new cultivars with broad adaptations. The main objective of this research is to understand the genetic basis of winter hardiness (WH) and fall dormancy (FD) in alfalfa and the association between the two traits. QTL analysis was conducted in a pseudo-testcross F1 population developed from two cultivars contrasting in FD (3010 with FD = 2 and CW 1010 with FD = 10). The mapping population was evaluated in three replications at two locations (Watkinsville and Blairsville, GA). FD levels showed low to moderate correlations with WH (0.22-0.57). Assessing dormancy in winter is more reliable than in the fall in southern regions with warm winters. The mapping population was genotyped using Genotyping-by-sequencing (GBS). Single dose allele SNPs (SDA) were used for constructing linkage maps. The parental map (CW 1010) consisted of 32 linkage groups spanning 2127.5 cM with 1377 markers and an average marker density of 1.5 cM/SNP. The maternal map (3010) had 32 linkage groups spanning 2788.4 cM with 1837 SDA SNPs with an average marker density of 1.5 cM/SNP. Forty-five significant (P < 0.05) QTLs for FD and 35 QTLs for WH were detected on both male and female linkage maps. More than 75% (22/28) of the dormancy QTL detected from the 3010 parent did not share genomic regions with WH QTLs and more than 70% (12/17) dormancy QTLs detected from CW 1010 parent were localized in different genomic regions than WH QTLs. These results suggest that the two traits have independent inheritance and therefore can be improved separately in breeding programs.