Cytogenetic and genomic characterization of a novel tall wheatgrass‑derived \u3ci\u3eFhb7\u3c/i\u3e allele integrated into wheat B genome

A novel tall wheatgrass-derived (Thinopyrum elongatum, genome EE) Fhb7 allele, designated Fhb7The2, was identified and integrated into the wheat B genome through a small 7B–7E translocation (7BS·7BL–7EL) involving the terminal regions of the long arms. Fhb7The2 conditions significant Type II resistance to Fusarium head blight (FHB) in wheat. Integration of Fhb7The2 into the wheat B genome makes this wild species-derived FHB resistance gene usable for breeding in both common and durum wheat. By contrast, other Fhb7 introgression lines involving wheat chromosome 7D can be utilized only in common wheat breeding programs, not in durum wheat. Additionally, we found that Fhb7The2 does not have the linkage drag of the yellow flour pigment gene that is tightly linked to the decaploid Th. ponticum-derived Fhb7 allele Fhb7Thp. This will further improve the utility of Fhb7The2 in wheat breeding. DNA sequence analysis identified 12 single nucleotide polymorphisms (SNPs) in Fhb7The2, Fhb7Thp, and another Th. elongatum-derived Fhb7 allele Fhb7The1, which led to seven amino acid conversions in Fhb7The2, Fhb7Thp, and Fhb7The1, respectively. However, no significant variation was observed in their predicted protein configuration as a glutathione transferase. Diagnostic DNA markers were developed specifically for Fhb7The2. The 7EL segment containing Fhb7The2 in the translocation chromosome 7BS·7BL–7EL exhibited a monogenic inheritance pattern in the wheat genetic background. This will enhance the efficacy of marker-assisted selection for Fhb7The2 introgression, pyramiding, and deployment in wheat germplasm and varieties

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

Intermediate wheatgrass [IWG; Thinopyrum intermedium (Host) Barkworth & D.R. Dewey subsp. intermedium] is being developed as a new perennial grain crop that has a large allohexaploid genome similar to that of wheat (Triticum aestivum 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 \u3e46%. Thus, by combining AM and genomic selection, we can effectively select the favorable QTL alleles for seed weight and size in IWG breeding populations

Using canopy spectral reflectance to estimate nitrogen use traits in hard winter wheat

Wheat nitrogen use efficiency must be improved to reduce the need for nitrogen (N) fertilizers. This study was conducted to determine if measurement of canopy spectral reflectance (CSR) could be used to non-destructively and indirectly select wheat genotypes with improved nitrogen use traits. Canopy spectral reflectance measurements were collected during grain fill in a 299 genotype trial planted near Ithaca, NE in 2012 and 2013. The objectives of this study were i) evaluate vegetation indices (VI) to determine the best index for indirectly evaluating nitrogen use (NU) traits in the context of a hard winter wheat breeding program ii) determine the ability of genomic prediction models to accurately predict VI phenotypes. Twenty-eight VI were calculated, and the relationship between VI and NU traits was investigated. Vegetation indices were highly heritable in both years and showed significant relationships with the NU traits anthesis biomass, anthesis N yield, mature biomass, grain N yield, grain yield, N harvest index, N utilization efficiency, N uptake efficiency and post anthesis N uptake. Two VIs, Maccioni and Boochs2, performed most consistently and were significantly related to several nitrogen use traits. The results of this study indicate that VIs in particular, Maccioni and Boochs2, could be used in wheat breeding program to non-destructively phenotype for nitrogen use traits. In order to utilize VI phenotypes across an entire breeding program, we proposed that genomic prediction models could be used to predict VI phenotypes based on genomic marker-phenotype relationships. Prediction of VI phenotypes would allow for indirect improvement of NU traits throughout a breeding program rather than in a single experimental trial with one generation of genotypes. Results of this study showed that VI traits can be used successfully in genomic selection models. Prediction accuracy for VIs was higher than the prediction accuracy of NU traits and grain yield. The Boochs2 index was predicted more accurately than the Maccioni index using both within year and across year cross validation. As a result, we recommend that the Boochs2 index be used in GP models to increase genetic gain for NU traits while reducing the time and labor costs of phenotyping

High Throughput Phenotyping in Plant Breeding

An introduction to plant breeding and high throughput phenotyping. This lesson outlines the steps and goals of the plant breeding process and identifies areas that can be improved with high throughput phenotyping methods. It also covers the steps necessary to collect and process UAV-based high throughput phenotyping data to make reliable plant breeding decisions. Lesson Objectives Explain plant breeding and the goals of the plant breeding process. Compare and contrast different High Throughput Phenotyping (HTP) methods and their potential to improve the plant breeding process. Outline the steps necessary to collect data using Unmanned Aerial Vehicle (UAV)-based HTP methods: pre-flight mission planning, pre-flight set up, and flight. Summarize the general process of storing, processing, and extracting information from raw UAV data and how it can be used to make reliable plant breeding decisions. Identify the limitations to HTP and the status of HTP in current breeding programs. Modules Lesson home Lesson Objectives Farming Success in a Changing World Plant Breeding History Plant Breeding Process Can New Technology Help Plant Breeding Decision Making? High Throughput Phenotyping Technology Plant Structure and Light Interactions High Throughput Phenotyping Sensors UAV Flight Ground-Truthing Data Analysis Data Processing Making Decisions Limitations to High Throughput Phenotyping Use of High Throughput Phenotyping Toda

Genetic Diversity of Field Pennycress (Thlaspi arvense) Reveals Untapped Variability and Paths Toward Selection for Domestication

Evaluation of genetic diversity within wild populations is an essential process for improvement and domestication of new crop species. This process involves evaluation of population structure and individual accessions based on genetic markers, growth habits, and geographic collection area. In this study, accessions of field pennycress were analyzed to identify population structure and variation in germplasm available for breeding. A total of 9157 genome-wide single nucleotide polymorphisms (SNPs) were identified among the 121 accessions analyzed, and linkage disequilibrium based pruning resulted in 3497 SNPs. Bayesian cluster analysis was implemented in STRUCTURE v2.3.4 to identify four population groups. These groups were confirmed based on principal components analysis and geographic origins. Pairwise diversity among accessions was evaluated and revealed considerable genetic variation. Notably, a subset of accessions from Armenia with exceptional genetic variation was identified. This survey is the first to report significant genetic diversity among pennycress accessions and explain some of the phenotypic differences previously observed in the germplasm. Understanding variation in pennycress accessions will be a crucial step for selection, breeding, and domestication of a new cash cover crop for cold climates

Novel Single-Nucleotide Variants for Morpho-Physiological Traits Involved in Enhancing Drought Stress Tolerance in Barley

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which resulted in 6913 high-quality SNPs. In conjunction with the SNP markers, the phenotypic data were subjected to a genome-wide association scan (GWAS) using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). The GWAS results indicated that 36 SNPs were significantly associated with the studied traits under DI and FI. Furthermore, eight markers were significant and common across DI and FI water regimes, while 14 markers were uniquely associated with the studied traits under DI. Under DI and FI, three (11_10326, 11_20042, and 11_20170) and five (11_20099, 11_10326, 11_20840, 12_30298, and 11_20605) markers, respectively, had pleiotropic effect on at least two traits. Among the significant markers, 24 were annotated to known barley genes. Most of these genes were involved in plant responses to environmental stimuli such as drought. Overall, nine of the significant markers were previously reported, and 27 markers might be considered novel. Several markers identified in this study could enable the prediction of barley accessions with optimal agronomic performance under DI and FI

Harvest aids did not advance maturity of non-shatter pennycress

Reliance on summer annual crops in the Upper Midwest results in fallow land from late fall through early spring, providing opportunities to integrate winter crops, such as pennycress (Thlapsi arvense L.), onto the landscape. Pennycress agronomics have primarily been studied using unimproved wild-type lines prone to seed shatter, resulting in significant yield loss if not harvested early. However, high plant and seed moisture complicates harvest and seed storage. A new breeding line with a reducedshatter mutation made it possible to use harvest aids to reduce plant moisture without the risk of seed loss. The objectives of this study were to quantify the reduction in pennycress seed and biomass moisture after applying a harvest aid and to assess the seed yield, oil content, and crude protein of the reduced-shatter line. This study was conducted over the 2018–2019 and 2019–2020 growing seasons with ‘“IO217” pennycress in Rosemount, MN. Seed moisture decreased to a similar level by harvest maturity regardless of treatment while swathing was the most effective method of reducing biomass moisture. Natural senescence decreased pennycress moisture content to a harvestable level at the same rate as treated plants, indicating that a harvest aid is not required at this time. Seed yield was two to six times higher than in studies using unimproved pennycress lines. Challenges associated with wild-type pennycress lines, such as uneven germination and late maturation, were prevalent in this study and further genetic improvement will be necessary to ensure successful pennycress production in the Upper Midwest

The performance of early-generation perennial winter cereals at 21 sites across four continents

A network of 21 experiments was established across nine countries on four continents and spanning both hemispheres, to evaluate the relative performance of early generation perennial cereal material derived from wheat, rye, and barley and to inform future breeding strategies. The experimental lines were grown in replicated single rows, and first year production and phenology characteristics as well as yield and persistence for up to three years were monitored. The study showed that the existing experimental material is all relatively short-lived