Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the VRN-A1 first intron (henceforth, RIP3) are associated with significant differences in heading time after a partial vernalization treatment. The ancestral winter VRN-A1 allele in 'Triple Dirk C' has one SNP in the RIP3 region (1_SNP) relative to the canonical RIP3 sequence, whereas the derived 'Jagger' allele has three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P < 0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 days difference) and after 3-weeks of vernalization (11 days difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 days, P < 0.001) and one experiment under field conditions (21 d, P < 0.0001). The RIP3 polymorphisms can be used by wheat breeders to develop winter wheat varieties adapted to regions with different duration or intensity of the cold season.
Many studies have evaluated the effectiveness of genomic selection (GS) using cross-validation within training populations; however, few have looked at its performance for forward prediction within a breeding program. The objectives for this study were to compare the performance of naïve GS (NGS) models without covariates and multi-trait GS (MTGS) models by predicting two years of F4:7 advanced breeding lines for three Fusarium head blight (FHB) resistance traits, deoxynivalenol (DON) accumulation, Fusarium damaged kernels (FDK), and severity (SEV) in soft red winter wheat and comparing predictions with phenotypic performance over two years of selection based on selection accuracy and response to selection. On average, for DON, the NGS model correctly selected 69.2% of elite genotypes, while the MTGS model correctly selected 70.1% of elite genotypes compared with 33.0% based on phenotypic selection from the advanced generation. During the 2018 breeding cycle, GS models had the greatest response to selection for DON, FDK, and SEV compared with phenotypic selection. The MTGS model performed better than NGS during the 2019 breeding cycle for all three traits, whereas NGS outperformed MTGS during the 2018 breeding cycle for all traits except for SEV. Overall, GS models were comparable, if not better than phenotypic selection for FHB resistance traits. This is particularly helpful when adverse environmental conditions prohibit accurate phenotyping. This study also shows that MTGS models can be effective for forward prediction when there are strong correlations between traits of interest and covariates in both training and validation populations.
Abstract ‘Hilliard’ (Reg. no. CV‐1163, PI 676271), a soft red winter (SRW) wheat ( Triticum aestivum L.) developed and tested as VA11W‐108 by the Virginia Agricultural Experiment Station, was released in March 2015. Hilliard was derived from the cross ‘25R47’/‘Jamestown’. Hilliard is widely adapted, from Texas to Ontario, Canada, and provides producers with a mid‐season, medium height, awned, semi‐dwarf ( Rht 2) cultivar that has very high yield potential, good straw strength, and intermediate grain volume weight and quality. It expresses moderate to high levels of resistance to most diseases prevalent in the eastern United States and Ontario. In the 2016–2018 USDA‐ARS Uniform SRW Wheat nurseries, Hilliard ranked first in grain yield in the southern nursery across all 3 yr (5,147–5,758 kg ha −1 ). In the uniform eastern nursery, it ranked first for grain yield in 2016 (6,159 kg ha −1 ) and 2017 (5,633 kg ha −1 ) and second in 2018 (5,515 kg ha −1 ). Grain volume weights of Hilliard were similar to overall trial averages in the uniform southern (73.4–75.2 kg hl −1 ) and eastern (70–75.8 kg hl −1 ) nurseries. Hilliard has soft grain texture with flour softness equivalent values varying from 58.1 to 61.7 g 100 g −1 . Straight grade flour yields on a Quadrumat Senior mill varied from 66.8 to 68.4 g kg −1 . Flour protein concentration varied from 7.0 to 9.1 g 100 g −1 and gluten strength from 108 to 128 g 100 g −1 , as measured by lactic acid solvent retention capacity. Cookie spread diameter varied from 18.3 to 18.6 cm.
Genotypic, phenotypic, and covariate SNP data collected on a panel of soft winter wheat grown in Blacksburg, Virginia and Warsaw, Virginia in the 2013-2014 and 2014-2015 winter wheat growing seasons as part of the USDA-NIFA Tritaceae Coordinated Agricultural Project (TCAP) mid-Atlantic allele-based breeding (ABB) panel.
Genotypic data is supplied in variant call format (VCF) files, both unimputed and following imputation with Beagle 4.1. Unimputed genotypic data was filtered to remove SNPs with minor allele frequency < 5%, > 50% missing data content, or with > 15% heterozygous calls. Following imputation, the genotypic data was refiltered for minor allele frequency and portion of heterozygous calls using the same thresholds listed above. The imputed data was thinned to only retain a single SNP in groups of SNPs in perfect linkage disequilibrium (r2 = 1).
Phenotypic data consists of one file of raw plot observations, and one file of fitted values generated by performing spatial corrections using the 'SpATS' package in R. Trait abbreviations are as follows: FLSG flag leaf stay green; GSQM grains per square meter; GW grain weight; HD heading date; HT plant height; MAT physiological maturity date; NDVI normalized-difference vegetation index at Zadok’s GS25; PROT wet chemistry-validated whole-grain protein content; SPH seeds per head; SSQM spikes per square meter; STARCH whole-grain starch content; TKW thousand kernel weight; TWT test weight; YLD grain yield. Covariate SNP data from KASP assays is provided in a VCF file, where a 0/0 denotes the homozygous wild-type state, 0/1 denotes the heterozygous state, and 1/1 denotes the homozygous "mutant" or "positive" state.
In humid and temperate areas, Septoria nodorum blotch (SNB) is a major fungal disease of common wheat ( Triticum aestivum L.) in which grain yield is reduced when the pathogen, Parastagonospora nodorum , infects leaves and glumes during grain filling. Foliar SNB susceptibility may be associated with sensitivity to P . nodorum necrotrophic effectors (NEs). Both foliar and glume susceptibility are quantitative, and the underlying genetics are not understood in detail. We genetically mapped resistance quantitative trait loci (QTL) to leaf and glume blotch using a double haploid (DH) population derived from the cross between the moderately susceptible cultivar AGS2033 and the resistant breeding line GA03185-12LE29. The population was evaluated for SNB resistance in the field in four successive years (2018–2021). We identified major heading date (HD) and plant height (PH) variants on chromosomes 2A and 2D, co-located with SNB escape mechanisms. Five QTL with small effects associated with adult plant resistance to SNB leaf and glume blotch were detected on 1A, 1B, and 6B linkage groups. These QTL explained a relatively small proportion of the total phenotypic variation, ranging from 5.6 to 11.8%. The small-effect QTL detected in this study did not overlap with QTL associated with morphological and developmental traits, and thus are sources of resistance to SNB.
Fusarium head blight (FHB) is a serious disease of wheat (Triticum aestivum L.) worldwide that has elicited a widespread resistance-breeding effort. One approach to breeding relies on deployment of exotic quantitative trait loci (QTL) from wheat outside North America. Germplasm line KY06C-11-3-10 (Reg. No. GP-965, PI 669817) is a soft red winter wheat that is a product of an accelerated backcrossing program performed jointly by the Kentucky Agricultural Experiment Station, Maryland Agricultural Experiment Station, Virginia Polytechnic Institute and State University, North Carolina State University, and the USDA–ARS. KY06C-11-3-10 carries exotic FHB resistance alleles from Chinese spring wheat ‘Ning7840’ at Fhb1, and at QTL on chromosomes 5A and 2DL. These QTL, backcrossed into ‘McCormick’—which itself has nonexotic, native moderate resistance—reduced FHB spike symptoms, percentage Fusarium-damaged kernels, and concentration of the mycotoxin deoxynivalenol (DON). KY06C-11-3-10 has additionally been selected for yield, test weight, heading date, height, milling and baking quality, and resistance to lodging. The combination of exotic resistance QTL, moderately resistant genetic background, widespread adaptation, and competitive agronomic and quality characteristics makes KY06C-11-3-10 a useful germplasm for wheat breeders.
‘Merl’ (Reg. No. CV‐1052, PI 658598) soft red winter (SRW) wheat ( Triticum aestivum L.), developed and tested as VA03W‐412 by the Virginia Agricultural Experiment Station, was released in March 2009. Merl was derived from the three‐way cross ‘Roane’/Pioneer variety 2643//‘38158’ (PI 619052). Merl is a broadly adapted, high‐yielding, mid‐season, moderately short, semidwarf ( Rht 2) cultivar having above‐average straw strength and milling and pastry‐baking qualities. Merl is resistant to powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer] and moderately resistant to stripe rust (caused by Puccinia striiformis Westend.). In Virginia, Merl ranked among the top five cultivars for grain yield with a 3‐yr (2007–2009) average of 5725 kg ha −1 Merl had a mean grain volume weight of 76.4 kg hL −1 across 22 environments, which was significantly ( P < 0.05) higher (1.9–3.0 kg hL −1 ) than that of the other top‐yielding cultivars. In USDA‐ARS Uniform Eastern SRW Wheat Nursery trials conducted at 29 locations, Merl ranked sixth among 46 entries for grain yield (5917 kg ha −1 ) and seventh for grain volume weight (76.0 kg hL −1 ) in 2006 and ranked second among 45 entries for grain yield (5529 kg ha −1 ) and sixth for grain volume weight (75.7 kg hL −1 ) in 2008. Merl has a soft grain texture, flour softness equivalent values from 57.5 to 60.8 g 100 g −1 , and straight‐grade flour yields from 70.5 to 71.5 g kg −1 The flour protein concentration (7.5–8.7 g 100 g −1 ) and gluten strength, assessed via lactic acid solvent retention capacity (101–104 g 100 g −1 ), of Merl are lower than average. These quality attributes contribute to Merl's above‐average pastry‐baking quality (cookie‐spread diameters of 17.93–18.93 cm).
Molecular markers are needed for enhancing the development of elite sweetpotato (Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and β-carotene content in a cross between 'New Kawogo' × 'Beauregard'. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H2) for storage root yield, dry matter, starch and β-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root β-carotene content was negatively correlated with dry matter (r = −0.59, P < 0.001) and starch (r = −0.93, P < 0.001) content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and β-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future.
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