Improvement of end‐use quality remains one of the most important goals in hard winter wheat (HWW) breeding. Nevertheless, the evaluation of end‐use quality traits is confined to later development ...generations owing to resource‐intensive phenotyping. Genomic selection (GS) has shown promise in facilitating selection for end‐use quality; however, lower prediction accuracy (PA) for complex traits remains a challenge in GS implementation. Multi‐trait genomic prediction (MTGP) models can improve PA for complex traits by incorporating information on correlated secondary traits, but these models remain to be optimized in HWW. A set of advanced breeding lines from 2015 to 2021 were genotyped with 8725 single‐nucleotide polymorphisms and was used to evaluate MTGP to predict various end‐use quality traits that are otherwise difficult to phenotype in earlier generations. The MTGP model outperformed the ST model with up to a twofold increase in PA. For instance, PA was improved from 0.38 to 0.75 for bake absorption and from 0.32 to 0.52 for loaf volume. Further, we compared MTGP models by including different combinations of easy‐to‐score traits as covariates to predict end‐use quality traits. Incorporation of simple traits, such as flour protein (FLRPRO) and sedimentation weight value (FLRSDS), substantially improved the PA of MT models. Thus, the rapid low‐cost measurement of traits like FLRPRO and FLRSDS can facilitate the use of GP to predict mixograph and baking traits in earlier generations and provide breeders an opportunity for selection on end‐use quality traits by culling inferior lines to increase selection accuracy and genetic gains.
Core Ideas
Improvement of end‐use quality is one of the most important goals in hard winter wheat breeding.
Multi‐trait genomic prediction (MTGP) can be used to predict end‐use quality traits that are difficult to phenotype.
Including rapid and NIR traits into MTGP improves prediction accuracy for end‐use quality traits.
MTGP can provide an opportunity for selection on end‐use quality traits in earlier generations.
Fusarium head blight (FHB), also known as scab, is a devastating fungal disease of wheat that causes significant losses in grain yield and quality. Quantitative inheritance and cumbersome phenotyping ...make FHB resistance a challenging trait for direct selection in wheat breeding. Genomic selection to predict FHB resistance traits has shown promise in several studies. Here, we used univariate and multivariate genomic prediction models to evaluate the prediction accuracy (PA) for different FHB traits using 476 elite and advanced breeding lines developed by South Dakota State University hard winter wheat breeding program. These breeding lines were assessed for FHB disease index (DIS), and percentage of Fusarium damaged kernels (FDK) in three FHB nurseries in 2018, 2019, and 2020 (TP18, TP19, and TP20) and were evaluated as training populations (TP) for genomic prediction (GP) of FHB traits. We observed a moderate PA using univariate models for DIS (0.39 and 0.35) and FDK (0.35 and 0.37) using TP19 and TP20, respectively, while slightly higher PA was observed (0.41 for DIS and 0.38 for FDK) when TP19 and TP20 (TP19 + 20) were combined to leverage the advantage of a large training population. Although GP with multivariate approach including plant height and days to heading as covariates did not significantly improve PA for DIS and FDK over univariate models, PA for DON increased by 20% using DIS, FDK, DTH as covariates using multi-trait model in 2020. Finally, we used TP19, TP20, and TP19 + 20 in forward prediction to calculate genomic-estimated breeding values (GEBVs) for DIS and FDK in preliminary breeding lines at an early stage of the breeding program. We observed moderate PA of up to 0.59 for DIS and 0.54 for FDK, demonstrating the promise in genomic prediction for FHB resistance in earlier stages using advanced lines. Our results suggest GP for expensive FHB traits like DON and FDK can facilitate the rejection of highly susceptible materials at an early stage in a breeding program.
ABSTRACT
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is one of the most serious diseases of wheat (Triticum aestivum L.) worldwide. The discovery of new Pgt races in Africa, Ug99 and ...its variants, brings a new threat to global wheat production. Pyramiding several stem rust resistance genes into adapted varieties as opposed to breeding varieties with a single resistance gene is considered a more effective method to combat new races, but the success of gene pyramiding depends on the availability of molecular markers tightly linked to resistance genes. Markers for Ug99‐effective genes, Sr2, Sr22, Sr26, Sr32, Sr35, Sr39, and Sr40, were evaluated for usefulness in marker‐assisted selection (MAS) of hard winter wheat (HWW) using 10 resistance gene donor lines, 17 recently released U.S. HWW varieties or breeding lines, and 20 advanced introgression lines. Markers XcsIH81‐BM and XcsIH81‐AG for Sr22, Xsr26#43 and XBE51879 for Sr26, Xbarc55 for Sr32, Xbarc51 for Sr35, Xrwg27 for Sr39, Xsr39#22r for Sr40, and csSr2‐derived single nucleotide polymorphism (SNP) marker for Sr2 are diagnostic for the set of HWW accessions evaluated in this study. These markers should be useful in marker‐assisted pyramiding of stem rust resistance genes to develop HWW cultivars with multiple gene resistance against Ug99 races.
Genetic dissection of complex traits by quantitative trait locus (QTL) analysis permits the understanding of the genotypic effects of QTL, interactions between QTLs, and QTL-by-environment ...interactions in wheat. This study aimed to identify the QTL linked to yield, its components, end-use quality traits including kernel, flour, and dough rheology, and related agronomic traits under dryland and irrigated conditions. A mapping population of 179 F2:6 recombinant inbred lines (RILs) derived from ‘TAM 111’/‘TX05A001822’ was evaluated for these traits to investigate their genetic stability and phenotypic plasticity using 2658 single nucleotide polymorphisms (SNPs) with 35 linkage groups. Traits associated with chromosome regions were detected for individual and across-environment QTL by inclusive composite interval mapping. A total of 30 QTL regions were identified, including 14 consistent QTLs mapped on 11 chromosomes and six pleiotropic QTLs mapped on 5 chromosomes. Three consistent QTLs in chromosomes 1A, 3B, and 6D might be novel. Three major QTLs with both consistent and pleiotropic effects were co-localized with known genes. The first QTL for dough mixing properties was physically clustered around Glu-D1 and had an phenotypic variation explained (PVE) up to 31.3%. The second QTL for kernel-related traits was physically close to the TaCWI-4A (cell wall invertase) gene, which influences the thousand kernel weight, heading date, and harvest index, with a PVE of up to 12.3%. The third QTL, which was colocalized with the TaCWI-5D gene for kernel traits, was identified with a PVE of 6.7%. Epistasis was also detected, but major QTLs were not involved in significant epistasis or interactions with environmental effects. The current study provided new information that is useful for enhanced wheat breeding, which will benefit from the deployment of the favorable alleles for end-use quality, yield, and other agronomic traits in wheat-breeding programs through marker-assisted selection.
Russian wheat aphid (RWA), Diuraphis noxia (Kurdjumov), is a significant insect pest of wheat (Triticum aestivum L.) and has had a major economic impact worldwide, especially on winter wheat in the ...western United States. Development of resistant cultivars remains the most viable method for RWA control, although the continuing emergence of new RWA biotypes virulent to deployed resistance genes reinforces the need for the discovery of new sources of resistance. Iranian wheat landrace accession PI 626580 has shown high levels of resistance to RWA biotypes 1 (RWA1) and 2 (RWA2), but the inheritance and chromosomal location of this resistance is unknown. The objectives of this study were to determine the inheritance of RWA2 resistance, identify closely linked markers, and map the chromosomal location of RWA2 resistance found in PI 626580. Bulked segregant analysis was conducted with a mapping population of 154 F2 individuals derived from a single plant selection made from PI 626580 and ‘Yuma’ (a susceptible wheat cultivar). Phenotypic segregation of RWA2 resistance suggested a single dominant gene, provisionally designated Dn626580. Linkage mapping analysis identified three simple sequence repeat (SSR) markers, Xbarc214, Xgwm473, and Xgwm437, proximally linked to Dn626580 near the centromere on the short arm of chromosome 7D at distances of 1.8, 5.0, and 8.2 cM, respectively. Dn626580, a new resistance gene found in PI 626580, could be used alone or by pyramiding with other resistance genes to develop cultivars with effective RWA resistance.
To understand the mechanisms of aluminum (Al) tolerance in wheat (Triticum aestivum L.), suppression subtractive hybridization (SSH) libraries were constructed from Al-stressed roots of two ...near-isogenic lines (NILs). A total of 1,065 putative genes from the SSH libraries was printed in a cDNA array. Relative expression levels of those genes were compared between two NILs at seven time points of Al stress from 15 min to 7 days. Fifty-seven genes were differentially expressed for at least one time point of Al treatment. Among them, 28 genes including genes for aluminum-activated malate transporter-1, ent-kaurenoic acid oxidase-1, β-glucosidase, lectin, histidine kinase, and phospoenolpyruvate carboxylase showed more abundant transcripts in Chisholm-T and therefore may facilitate Al tolerance. In addition, a set of genes related to senescence and starvation of nitrogen, iron, and sulfur, such as copper chaperone homolog, nitrogen regulatory gene-2, yellow stripe-1, and methylthioribose kinase, was highly expressed in Chisholm-S under Al stress. The results suggest that Al tolerance may be co-regulated by multiple genes with diverse functions, and those genes abundantly expressed in Chisholm-T may play important roles in enhancing Al tolerance. The down-regulated genes in Chisholm-S may repress root growth and restrict uptake of essential nutrient elements, and lead to root senescence.
Vicilin type (8S) and basic 7S globulins and legumin type (11S) globulins were isolated from mungbean Vigna radiata (L.) Wilczek. The native molecular weights of the different globulin types were ...360000 for legumin, 200000 for vicilin, and 135000 for basic 7S. Some of the 8S globulin apparently complexed and coeluted with the 11S on gel filtration. On SDS-PAGE, 11S was composed of two bands of 40000 and 24000, 8S was composed of 60000, 48000, 32000, and 26000 bands, and basic 7S was composed of 28000 and 16000 bands. The percent composition of total globulins was estimated to be as follow: 8S, 89%; basic 7S, 3.4%; and 11S, 7.6%. The basic 7S and 11S but not the 8S globulins were found to have disulfide bonds. The presence of carbohydrates by conjugated peroxidase reaction was observed in all bands of 8S, the acidic polypeptide of basic 7S, and its complex but not in 11S. The 28000 basic 7S band and its 42000 complex and the first three major bands of 8S cross-reacted with antibodies to all types of soybean conglycinin subunits (α, α‘, and β), whereas the fourth band cross-reacted only with the anti-β subunit. None of the mungbean globulins cross-reacted with anti-soybean glycinin. Basic 7S was found to be easily extracted with 0.15 M NaCl, 11S was extracted with 0.35 M NaCl,and 8S was extracted over a wide range of NaCl concentrations. The N-terminal sequences of the different subunits/fragments of the globulins were determined and found to have strong homology with storage proteins of other legumes and crops. Keywords: Globulins; mungbean proteins; vicilin; legumin; storage proteins
We have previously cloned and characterized the cDNAs of three isoforms of the 8S globulin of mungbean, expressed the major 8Sα isoform in Escherichia coli, and purified and successfully crystallized ...it (Bernardo, A. E. N.; Garcia, R. N.; Adachi, M.; Angeles, J. G. C.; Kaga, A; Ishimoto, M.; Utsumi, S.; Tecson-Mendoza, E. M. J. Agric. Food Chem. 2004, 52, 2552−2560). Herein, we report the physicochemical and emulsifying properties of the native 8S and recombinant 8Sα globulin or vicilin. The circular dichroism spectra analysis of the native 8S and recombinant 8Sα globulins revealed that the recombinant 8Sα formed a secondary structure close to that of the native 8S. Further, gel filtration analysis showed that 8Sα was able to assemble into trimers. The native 8S and recombinant 8Sα globulins were soluble at pH 3.4 and at pH 7.4−9.0 at low ionic strength, μ = 0.08. Interestingly, the native 8S was more soluble at pH 7.0 and pH 7.4 than the recombinant 8Sα at μ = 0.08. Both forms were very soluble at pH 3.4−9.0 at high ionic strength, μ = 0.50. The native form exhibited a higher T m (69.2, 79.5, and 83.8 °C) than the recombinant form (65.6, 71.6, 77.5 °C) at μ = 0.1, 0.2, and 0.5, respectively. The recombinant form was found to have greater surface hydrophobicity than the native form. There was little difference in the emulsifying ability between the native 8S and 8Sα at pH 3.4 and pH 7.6. The results indicate that the presence of N-linked glycans is not essential in the assembly and stable conformation of the mungbean vicilin. However, the N-linked glycans might have contributed to the higher solubility at low ionic strength, greater thermal stability, and decreased surface hydrophobicity of the native vicilin as compared to the recombinant 8Sα. On the other hand, the N-linked glycans showed little effect on the emulsifying ability of the protein. Keywords: Functional properties; 8S globulins; mungbean; N-linked glycans; recombinant; physicochemical properties; vicilin; Vigna radiata
Key message
A new gene for adult plant leaf rust resistance in wheat was mapped to chromosome 3BL. This gene was designated as
Lr77
.
‘Santa Fe’ is a hard red winter cultivar that has had ...long-lasting resistance to the leaf rust fungus,
Puccinia triticina
. The objective of this study was to determine the chromosome location of the adult plant leaf rust resistance in Santa Fe wheat. A partial backcross line of ‘Thatcher’ (Tc) wheat with adult plant leaf rust resistance derived from Santa Fe was crossed with Thatcher to develop a Thatcher//Tc*2/Santa Fe F
6
recombinant inbred line (RIL) population. The RIL population and parental lines were evaluated for segregation of leaf rust resistance in three field plot tests and in an adult plant greenhouse test. A genetic map of the RIL population was constructed using 90,000 single-nucleotide polymorphism (SNP) markers with the Illumina Infinium iSelect 90K wheat bead array. A significant quantitative trait locus for reduction of leaf rust severity in all four tests was found on chromosome 3BL that segregated as a single adult plant resistance gene. The RILs with the allele from the resistant parent for SNP marker
IWB10344
had lower leaf rust severity and a moderately resistant to moderately susceptible response compared to the susceptible RILs and Thatcher. The gene derived from Santa Fe on chromosome 3BL was designated as
Lr77
. Kompetitive allele-specific polymerase chain reaction assay markers linked to
Lr77
on 3BL should be useful for selection of wheat germplasm with this gene.
Key message
The novel, leaf rust seedling resistance gene,
Lr81
, was identified in a Croatian breeding line and mapped to a genomic region of less than 100 Kb on chromosome 2AS.
Leaf rust, caused by
...Puccinia triticina
, is the most common and widespread rust disease in wheat. Races of
Puccinia triticina
evolve rapidly in the southern Great Plains of the USA, and leaf rust resistance genes often lose effectiveness shortly after deployment in wheat production. PI 470121, a wheat breeding line developed by the University of Zagreb in Croatia, showed high resistance to
Puccinia triticina
races collected from Oklahoma, suggesting that PI 470121 could be a leaf rust resistance source for the southern Great Plains of the USA. Genetic analysis based on an F
2
population and F
2:3
families derived from the cross PI 470121 × Stardust indicated that PI 470121 carries a dominant seedling resistance gene, designated as
Lr81
. Linkage mapping delimited
Lr81
to a genomic region of 96,148 bp flanked by newly developed KASP markers
Xstars-KASP320
and
Xstars-KASP323
on the short arm of chromosome 2A, spanning 67,030,206–67,132,354 bp in the Chinese Spring reference assembly (IWGSC RefSeq v1.0). Deletion bin mapping assigned
Lr81
to the terminal bin 2AS-0.78–1.00. Allelism tests indicated that
Lr81
is a distinctive leaf rust resistance locus with the physical order
Lr65
-
Lr17
-
Lr81
. Marker-assisted selection based on a set of markers closely linked to leaf rust resistance genes in PI 470121 and Stardust enabled identification of a recombinant inbred line RIL92 carrying
Lr81
only.
Lr81
is a valuable leaf rust resistance source that can be rapidly introgressed into locally adapted cultivars using KASP markers
Xstars-KASP320
and
Xstars-KASP323
.
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