The spring wheat (Triticum aestivum L.) line ‘Copio’ has exhibited high level of adult plant resistance (APR) to the leaf rust (Puccinia triticina) pathogen in Mexico during field evaluations. To elucidate the genetic basis of leaf rust resistance in Copio, 176 F₄‐derived F₆‐recombinant inbred lines (RILs) from a cross of wheat lines ‘Apav’ and Copio were phenotyped in the field for two seasons in the United States and Mexico. A total of 762 genotyping‐by‐sequencing (GBS) single nucleotide polymorphic (SNP) markers were used to develop linkage maps. Composite interval mapping identified seven quantitative trait loci (QTL), all contributed by Copio. Three QTL on chromosome arms 1BL (QLr.umn‐1B), 2AS (QLr.umn‐2A), and 3BS (QLr.umn‐3B) were consistently expressed across all four environments. The QTL on 1BL represents Lr46, which is a pleiotropic APR gene, while the QTL on 2AS is colocated to the Lr37 gene in the 2NS/2AS translocation fragment. The QTL on 3BS, mapped to the Sr2/Yr30/Lr27 genomic region, is more likely to be a unique locus conferring APR to leaf rust races because all phenotyping environments had Lr27 virulent pathotypes. Moreover, the functionality of Lr27 is complimented by Lr31 on chromosome 4BS, which is lacking in both parents. Marker haplotypes identified seven RILs carrying a combination of resistance alleles at all three loci. This combination reduced leaf rust coefficient of infection up to 52 and 36% in the Mexican and U.S. environments, respectively. This study reports the complex genetic mechanism of APR to leaf rust in Copio and its importance as a potential resistance source for gene pyramiding through recombination breeding.

Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line ‘Copio’. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent ‘Apav’ with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping using 762 genotyping-by-sequencing markers identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37, and Yr17. Three quantitative trait loci (QTLs) were mapped on chromosomes 2B, two QTLs on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D, and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27 to 39% less stem rust coefficient of infection in all field environments compared with RILs with none of these genes, and this gene combination was most effective in the U.S. environments. We conclude that Copio carries several genes that provide both race-specific and non–race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.

Phosphorus (P) and nitrogen (N) deficiencies are major yield-limiting factors for wheat (Triticum aestivum) production worldwide, particularly in the acidic soils of the southern Great Plains of North America. In this study, we report that the transcription factor gene TaMYB-D7 is responsible for a major quantitative trait locus controlling purple leaf color. The wheat cultivar “2174” showed purple coleoptiles regardless of P status, whereas “Jagger” did not, even under P limitation. The 2 cultivars differed by 1 amino acid in TaMYB-D7: Gly-50 in TaMYB-D7b (encoded by the 2174 allele) and Ser-50 in TaMYB-D7a (encoded by the Jagger allele). We used genome editing to inactivate all 3 TaMYB7 homoeologs in cv. 2174. The resulting edited wheat plants did not accumulate purple pigments throughout their life cycle, validating the functions of TaMYB-7Db associated with the purple phenotype. In the TaMYB7-edited plants, chalcone synthase 2-like (TaCHSL2), which may be involved in anthocyanidin biosynthesis and metabolism, was dramatically downregulated, suggesting that TaMYB7 induces its transcription. We also discovered that the expression of TaMYB7 and TaCHSL2 was upregulated by P but downregulated by N. Lastly, we developed a Kompetitive Allele Specific PCR (KASP) marker to facilitate the genotyping of TaMYB-D7b, which can be used for marker-assisted breeding. Our results provide insight into nutrient use efficiency in wheat.

Genetic improvement in wheat yield is the most focused research area for the breeding community to ensure food security and sustainable production. Wheat kernel traits and biomass are considered key contributors to enhance crop yield. A set of 264 doubled haploid (DH) lines mainly derived from two popular Texas wheat cultivars, TAM 114 and TAM 204, were developed at the AgriLife Research Center in Amarillo. The other parents are widely adopted and improved cultivars from the Southern Great Plains. Lines were evaluated in two field environments (Bushland-irrigated & Bush-land-dryland) planted in alpha lattice design during the 2020 crop season. Kernel traits (seed length, width, area, perimeter, and 1000 kernel weight) were collected using the hp Scanjet G4010 photo scanner for image capturing and GrainScan software for image analysis. This procedure offered a high throughput, precise, robust, and cost-effective seed phenotyping platform. Biomass parameters (plant weight, head count, head weight) were collected and processed manually. For genotyping genomic libraries were prepared and sequenced on Illumina NovaSeq 6000 to generate paired end reads of 150 bp. For single nucleotide polymorphism (SNP) calling, sequences were aligned to the IWGSC RefSeq genome assembly v2.1 using the Burrows Wheeler Aligner. The SNP filtration was performed at 50% missing data and 5% minor allele frequency. Finally, a set of 59842 polymorphic markers were retained for genetic analysis. To investigate the marker-trait association and the genomic regions, four genome-wide-association study (GWAS) models were implemented using the R package ‘Genome Association and Prediction Integrated Tool’ (GAPIT). Based on the Bonferroni correction < 8.41E-07 was used as a threshold to declare maker trait associations (MTA) significant. The BLINK model identified 12 MTA on chromosomes 1A, 2A, 2B, 4A, 4B, and 6B. 45% of the lines carried S2A_251496962 marker for the seed perimeter, while 42% and 39% lines carried S2A_498737202 and S2B_792756832 makers for 1000 KW and seed width, respectively. The identified MTA might be representing some known/major genes which need fur-ther confirmation.

Background: Improving grain yield in wheat remains a top priority, requiring integrated breeding and genetic strategies. This complexity poses a major challenge, driven by quantitative polygenic inheritance, environmental influence, and intricate genetic interactions. We investigated genetic factors and their interactions for agronomic and yield traits in two high-yielding winter wheat cultivars adapted to the US Southern Great Plains. Methods: A bi-parental mapping population consisting of 221 F₇ recombinant inbred lines (RIL) derived from ‘TAM 204’ and ‘Iba’ was evaluated for three years in 11 Texas environments. Both parents and RIL population were genotyped on Illumina NovaSeq 6000 and sequences were aligned to IWGSC RefSeq v1.0 using Bowtie2 for SNP calling. For QTL analyses, each trait was analyzed by individual environment, across multiple environments and mega-environments. Results: A total of 86 QTL were mapped for five traits and among them 32 were consistent in more than one environment or analysis. Among consistent QTL, four were pleiotropic to more than one agronomic or yield traits mapped on chromosomes 2B (57.18, 59.47 Mb) and 2D (29.34, 40.64 Mb). The consistent QTL on chromosome 2D (29.34 Mb) was pleiotropic to GYLD, DTH, TW, TKW and explained maximum phenotypic variation for all traits, representing photoperiod gene (Ppd-D1). Another QTL on chromosome 2D (40.64 Mb) was pleiotropic to GYLD and TW and based on the physical position comparisons it likely reflects a unique locus in Iba. The pleiotropic consistent QTL Qgyld.tamu.2B.59 from TAM 204 represents Ppd-B1 gene. Moreover, it is more likely that Qdth.tamu.5B.575 represents the Vrn-B1 gene in Iba. A total of 23 digenic epistatic interactions involved consistent QTL for all traits. Amongst these, epistatic interactions between the consistent QTL on 2B (57.18 Mb) and 2D (29.34 Mb) were observed for GYLD, DTH and TKW. Conclusions: Our findings revealed key allelic diversity and interaction effects in elite wheat cultivars, paving the way for marker development for identified pleiotropic loci and implementation in marker-assisted selection and recombination breeding.

The first hexaploid bread wheat reference genome from Chinese Spring was released in 2018 by the International Wheat Genome Sequencing Consortium and is considered as the industry standard reference. To explore the effects of different reference genomes on variant discovery, 29 hexaploid bread wheat ( Triticum aestivum L.) cultivars from the Southern Great Plains of the United States with varying whole genome sequencing depth were aligned to three reference genomes. The reference genomes varied in evolutionary similarity to the cohort of the germplasm analyzed: (1) Jagger, a Kansas State University cultivar, a reference with high similarity, (2) Chinese Spring, a Chinese landrace, the current industry standard, (3) Durum‐ tauschii , an “in silico” hybridization of the reference genomes of tetraploid durum wheat and wild Aegilops tauschii , for an unrepresentative reference. The Jagger reference genome retained more informative variants after filtering. Synteny regions and large introgressions were identified by read alignment coverage, using diverse reference genomes to identify lines containing Aegilops ventricosa (2N ^v S), 1AL:1RS and 1BL:1RS ( Secale cereale ) rye translocations, and a 2.8 Mb contig from TAM 112 known to contain a haplotype harboring greenbug [ Schizaphis graminum (Rondani)] resistance gene Gb3 . The choice of reference genome is important, but any single reference can induce bias. This study with US Southern Great Plains germplasm demonstrated the importance of multiple reference genomes to capture genetic diversity.