Second Chromosome Research Articles

BSA-seq and transcriptome analysis reveal GhDSA05 as a candidate gene responsible for sensitivity to defoliants in Gossypium hirsutum L.

With the development of machine-harvested cotton, the application of defoliants is a key technology that can promote defoliation and reduce impurities in cotton fibers. Therefore, sensitivity to defoliants is a very important trait in machine-harvested cotton. In this study, to uncover the genetic basis of defoliant sensitivity in cotton, bulked segregant analysis by sequencing was used with a F2 population derived from Xinluzao 57 (XLZ57, defoliant sensitive) and Nan 2 (N2, defoliant insensitive) to mapped the quantitative trait locus (QTL) to a 3.66-Mb interval at chromosome A05. Then, 284 F2 individuals were used to validate and narrow the QTL to a 1.6-Mb interval and was named qSD-A05. To identify the candidate genes, dynamic transcriptome analysis of the abscission zone (AZ) in XLZ57 and N2 after defoliant treatment was performed. A total of 132 and 142 common differentially expressed genes (DEGs) were identified at all time points in N2 and XLZ57, respectively, and were enriched in the defense response pathway and abscisic acid-activated signaling pathway. More importantly, 15 DEGs were identified in the qSD-A05 interval, among which, Ghi_A05G23601 was significantly upregulated after defoliant treatment. There were multiple variants between N2 and XLZ57, including missense and frameshift mutations. Therefore, Ghi_A05G23601 was regarded as the key candidate gene and was named GhDSA05, which encodes a Facilitator superfamily transporter protein. To verify the function of GhDSA05, virus-induced gene silencing was performed, which showed that the GhDSA05-silenced plants exhibited decreased defoliant sensitivity. Additionally, the expression of organ abscission-related genes was downregulated in the GhDSA05-silenced plants. In summary, GhDSA05 positively regulates the formation of AZ under defoliant treatment and promotes leaf abscission in cotton. The results of this study not only enhance our knowledge of the defoliation mechanism of cotton but also provide a target for the genetic improvement of defoliant sensitivity.

Identification and validation of two quantitative trait loci showing pleiotropic effect on multiple grain-related traits in bread wheat (Triticum aestivum L.).

QKl/Tgw/Gns.yaas-2D associates with KL, TGW, and GNS, and QKl/Tgw.yaas-5A associates with KL and TGW. Significantly pleiotropic and additive effects of these two QTL were validated. The YM5 allele both at QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A was proved to be the best allelic combination for improving yield potential. Kernel length (KL), kernel width (KW), thousand grain weight (TGW), and grain number per spike (GNS) play important roles in the yield improvement of wheat. In this study, one recombinant inbred line (RIL) derived from a cross between Yangmai 5 (YM5) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) associated with KL, KW, TGW, and GNS across three years. Two pleiotropic QTL namely QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A were located in two genomic regions on chromosomes 2D and 5A, respectively. Breeder-friendly Kompetitive Allele-Specific PCR (KASP) markers for QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A were developed and validated in a set of 246 wheat cultivars/lines. Analysis of allelic combinations indicated that the YM5 allele both at QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A is probably the best one to promote TGW, GNS, and grain weight per spike. Based on the analysis of gene annotation, sequence variations, expression patterns, and GO enrichment, twenty-five and twenty-four candidate genes of QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A, respectively, were identified. These results provide the basis of fine-mapping the target QTL and marker-assisted selection in wheat yield-breeding programs.

Genetic mapping of QTLs for resistance to bacterial leaf streak in hexaploid wheat.

Robust QTLs conferring resistance to bacterial leaf streak in wheat were mapped on chromosomes 3B and 5A from the variety Boost and on chromosome 7D from the synthetic wheat line W-7984. Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa poses a significant threat to global wheat production. High levels of BLS resistance are rare in hexaploid wheat. Here, we screened 101 diverse wheat genotypes under greenhouse conditions to identify new sources of BLS resistance. Five lines showed good levels of resistance including the wheat variety Boost and the synthetic hexaploid wheat line W-7984. Recombinant inbred populations derived from the cross of Boost × ND830 (BoostND population) and W-7984 × Opata 85 (ITMI population) were subsequently evaluated in greenhouse and field experiments to investigate the genetic basis of resistance. QTLs on chromosomes 3B, 5A, and 5B were identified in the BoostND population. The 3B and 5A QTLs were significant in all environments, but the 3B QTL was the strongest under greenhouse conditions explaining 38% of the phenotypic variation, and the 5A QTL was the most significant in the field explaining up to 29% of the variation. In the ITMI population, a QTL on chromosome 7D explained as much as 46% of the phenotypic variation in the greenhouse and 18% in the field. BLS severity in both populations was negatively correlated with days to heading, and some QTLs for these traits overlapped, which explained the tendency of later maturing lines to have relatively higher levels of BLS resistance. Markers associated with the QTLs were converted to KASP markers, which will aid in the deployment of the QTLs into elite lines for the development of BLS-resistant wheat varieties.

Genome‐wide association study for powdery mildew resistance in CIMMYT's spring wheat germplasm

AbstractPowdery mildew (PM), caused by Blumeria graminis f. sp. tritici (Bgt), is a foliar disease of wheat (Triticum aestivum) that adversely affects both grain yield and quality. Growing resistant cultivars offers an effective and environmentally sustainable solution to managing PM. However, relying on the same genetic source of resistance can lead to resistance breakdown as Bgt isolates rapidly evolve. To mitigate this, identifying novel resistance sources is crucial. In this study, 225 diverse wheat genotypes were evaluated at adult plant stage in disease nurseries over the three crop seasons (2018/2019, 2019/2020 and 2020/2021). Using disease and genotyping data from 12,160 single‐nucleotide polymorphism (SNP) markers, a genome‐wide association study (GWAS) was conducted to identify novel resistance loci. We identified 22 marker loci significantly (at p < 0.005) associated with PM resistance, distributed across 14 wheat chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 5D, 6A, 7A and 7B). Of these, seven loci overlap with previously identified regions, while the remaining 15 loci represent novel regions reported for the first time in this study. The identified SNP markers have significant potential for wheat breeding programmes, as they can accelerate the development of PM‐resistant cultivars through marker‐assisted selection.

Genome‐Wide Association Mapping and Genomic Prediction of Septoria nodorum Blotch Resistance in Central European Winter Wheat (Triticum aestivum L.)

ABSTRACTSeptoria nodorum blotch (SNB) is a fungal disease of wheat caused by the necrotrophic fungus Parastagonospora nodorum (Berk.), considered as one of the most devastating fungal diseases affecting winter wheat (Triticum aestivum L.). The complex inheritance of resistance to SNB poses significant challenges to breeding programmes. Improving selection precision and identifying novel resistance QTLs are crucial for enhancing SNB resistance. This study investigated strategies for crop genetic improvement, including genome‐wide association mapping (GWAS) and genomic prediction (GP), within a practical breeding programme. A population of 1500 winter wheat breeding lines was phenotyped for SNB resistance over 5 years across 19 geographical locations under natural infection conditions. Despite highly unbalanced breeder's data, medium to high heritabilities for SNB resistance were achieved. GWAS identified 11 significant marker‐trait associations for SNB resistance across Chromosomes 2A, 2B, 4B, 4D, 5D and 7B. GP fivefold cross‐validation analysis revealed a predictive ability of 0.52 for SNB resistance. The resistant wheat genotypes and SNP markers identified in this study will be valuable assets for future breeding efforts to enhance SNB resistance in wheat.

Quantitative Trait Loci Mapping for Powdery Mildew Resistance in Wheat Genetic Population

Background/Objectives: Powdery mildew is a prevalent wheat disease that affects yield and quality. The characterization and fine mapping of genes associated with powdery mildew resistance can benefit marker-assisted breeding. Methods: In this study, quantitative trait loci (QTL) associated with powdery mildew were mapped using a high-density 35K DArT genetic linkage map developed from a population of double haploid lines (DHs) created by crossing “Jinmai 33 (a highly resistance line) with Yannong 19 (a highly susceptible line)”. Results: Three stable QTLs for powdery mildew were identified on chromosomes 1B, 2B, and 6A combined with the composite interval graphing method and multiple interval mapping, explaining phenotypic variations (PVE) that range from 4.98% to 13.25%. Notably, Qpm.sxn-1B and Qpm.sxn-2B were identified across three environments, with the PVE ranging from 9.37% to 13.25% and from 4.98% to 5.23%, respectively. The synergistic effects of these QTLs were contributed by the parental line “Jinmai 33”. Qpm.sxn-1B was the major stable QTL, and Qpm.sxn-2B was close to Pm51. Furthermore, Qpm.sxn-6A was identified in two environments, accounting for PVE values of 7.13% and 7.65%, respectively, with the resistance effects originating from the male parent. Remarkably, this locus has not been reported previously, indicating that Qpm.sxn-6A represents a newly dis-covered QTL governing powdery mildew genes. Conclusions: Five molecular markers available for mark-er-assisted selection were selected for tracking Qpm.sxn-1B and Qpm.sxn-2B in the program. The identification of this novel newly discovered QTL and markers reported in this study will be useful for marker-assisted selection of powdery mildew resistance.

Genetic dissection and validation of a stable QTL for grain roundness on chromosome 5A in bread wheat (Triticum aestivum L.)

Genetic dissection and validation of a stable QTL for grain roundness on chromosome 5A in bread wheat (Triticum aestivum L.)

A novel root hair mutant, srh1, affects root hair elongation and reactive oxygen species levels in wheat.

Root hairs are single-celled projections on root surfaces, critical for water and nutrient uptake. Here, we describe the first short root hair mutant in wheat (Triticum aestivum L.), identified in a mutagenized population and termed here short root hair 1 (srh1). While the srh1 mutant can initiate root hair bulges, lack of subsequent extension results in very short root hairs. Due to its semi-dominant nature, heterozygous lines displayed intermediate root hair lengths compared to wild-type. Bulked segregant analysis in a BC1F3 segregating population genotyped via exome capture sequencing localized the genetic control of this mutant to a region on the long arm of chromosome 3A. Via RNA sequencing and bioinformatic analysis, we identified two promising candidate genes. The first was a respiratory burst oxidase homolog (RBOH) encoding gene TaNOX3-A, orthologous to RBOH genes controlling root hair elongation in rice (OsNOX3) and maize (ZmRTH5), that carries a missense mutation in a conserved region of the predicted protein. RBOHs are membrane bound proteins that produce reactive oxygen species (ROS) which trigger cell wall extensibility, allowing subsequent root hair elongation. Notably, reduced ROS levels were observed in srh1 root hair bulges compared to wild-type. The second candidate was the calreticulin-3 encoding gene TaCRT3-A, located within the wider srh1 interval and whose expression was significantly downregulated in srh1 root tissues. The identification of a major effect gene controlling wheat root hair morphology provides an entry point for future optimization of root hair architecture best suited to future agricultural environments.

Genome-wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits.

Strawberries (Fragaria sp.) are cherished for their organoleptic properties and nutritional value. However, breeding new cultivars involves the simultaneous selection of many agronomic and fruit quality traits, including fruit firmness and extended postharvest life. The strawberry germplasm collection here studied exhibited extensive phenotypic variation in 26 agronomic and fruit quality traits across three consecutive seasons. Phenotypic correlations and principal component analysis revealed relationships among traits and accessions, emphasizing the impact of plant breeding on fruit weight and firmness to the detriment of sugar or vitamin C content. Genetic diversity analysis on 124 accessions using 44,408 markers denoted a population structure divided into six subpopulations still retaining considerable diversity. Genome-wide association studies for the 26 traits unveiled 121 significant marker-trait associations distributed across 95 quantitative trait loci (QTLs). Multiple associations were detected for fruit firmness, a key breeding target, including a prominent locus on chromosome 6A. The candidate gene FaPG1, controlling fruit softening and postharvest shelf life, was identified within this QTL region. Differential expression of FaPG1 confirmed its role as the primary contributor to natural variation in fruit firmness. A kompetitive allele-specific PCR assay based on the single nucleotide polymorphism (SNP) AX-184242253, associated with the 6A QTL, predicts a substantial increase in fruit firmness, validating its utility for marker-assisted selection. In essence, this comprehensive study provides insights into the phenotypic and genetic landscape of the strawberry collection and lays a robust foundation for propelling the development of superior strawberry cultivars through precision breeding.

Genome-Wide Identification and Expression Analysis of SNAP Gene Family in Wheat

Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution, physicochemical properties, conserved motifs, and cis-acting elements of the TaSNAP family members. Results: The TaSNAP family comprises members that encode proteins ranging between 120 and 276 amino acids, with isoelectric points spanning from 4.87 to 7.92. Phylogenetic analysis elucidated the categorization of the eight TaSNAP into three distinct subfamilies, wherein members of the same subfamily display marked similarities in their gene structures. Chromosomal mapping revealed the distribution of TaSNAP family members across chromosomes 2A, 2B, 2D, 7A, 7B, and 7D. Utilizing the Plant CARE tool, we identified ten elements linked to plant hormones and four associated with stress responses. Expression analysis via qRT-PCR was performed to assess the levels of the eight TaSNAP genes in various tissues and under diverse abiotic stress conditions. The results indicated heightened expression of most genes in roots compared to spikes. Notably, under ABA stress, the majority of genes exhibited upregulation, whereas certain genes were downregulated under PEG stress, implying a substantial role for SNAP protein in wheat growth and development. Conclusions: This study conducted a comprehensive bioinformatics analysis of each member of the wheat SNAP family, laying a crucial foundation for future functional investigations.

The effect of T. aestivum chromosomes 1A and 1D on fertility of alloplasmic recombinant (H. vulgare)-T. aestivum lines depending on cytonuclear compatibility.

The effect of T. aestivum L. chromosomes 1A and 1D on fertility of recombinant bread wheat allolines of the same origin carrying the cytoplasm of barley H. vulgare L. and different levels of cytonuclear compatibility was studied. Alloline L-56 included mainly fully sterile (FS) and partially sterile (PS) plants, alloline L-57 included partially fertile (PF) plants and line L-58 included fertile (F) ones. Analysis of morphobiological traits and pollen painting indicated complete or partial male sterility in plants of allolines L-56 and L-57. To differentiate genotypes with cytonuclear coadaptation and genotypes with cytonuclear incompatibility, PCR analysis of the 18S/5S mitochondrial (mt) repeat was performed. Heteroplasmy (simultaneous presence of barley and wheat mtDNA copies) was found in FS, PS, PF and some F plants, which was associated with a violation of cytonuclear compatibility. Wheat-type homoplasmy (hm) was detected in the majority of the fertile plants, which was associated with cytonuclear coadaptation. The allolines used as maternal genotypes were crossed with wheat-rye substitution lines 1R(1A) and 1R(1D). In F1, all plants of PF×1R(1A) and PF×1R(1D) combinations were fertile, and in F2, a segregation close to 3 (fertile) : 1 (sterile) was observed. These results showed for the first time that chromosomes 1A and 1D carry one dominant Rf gene, which controls the restoration of male fertility of bread wheat carrying the cytoplasm of H. vulgare. All plants of F1 combinations FS×1R(1A), FS×1R(1D), PS×1R(1A), PS×1R(1D) were sterile, which indicates that a single dose of genes localized on wheat chromosomes 1A or 1D is not enough to restore male fertility in FS and PS plants. All plants of hybrid combinations F(hm)×1R(1A) and F(hm)×1R(1D) in both F1 and F2 were fertile, that is, fertility of allolines with cytonuclear coadaptation does not depend on wheat chromosomes 1A and 1D.

A novel strategy to map a locus associated with flowering time in canola (Brassica napus L.).

Flowering time is an important agronomic trait for canola breeders, as it provides growers with options for minimizing exposure to heat stress during flowering and to more effectively utilize soil moisture. Plants have evolved various systems to control seasonal rhythms in reproductive phenology including an internal circadian clock that responds to environmental signals. In this study, we used canola cultivar 'Westar' as a recurrent parent and canola cultivar 'Surpass 400' as the donor parent to generate a chromosome segment substitution line (CSSL) and to map a flowering time locus on chromosome A10 using molecular marker-assisted selection. This CSSL contains an introgressed 4.6 mega-bases (Mb) segment (between 13 and 17.6Mb) of Surpass 400, which substantially delayed flowering compared with Westar. To map flowering time gene(s) within this locus, eight introgression lines (ILs) were developed carrying a series of different lengths of introgressed chromosome A10 segments using five co-dominant polymorphic markers located at 13.5, 14.0, 14.5, 15.0, 15.5, and 16.0Mb. Eight ILs were crossed with Westar reciprocally and flowering time of resultant 16 F1 hybrids and parents were evaluated in a greenhouse (2021 and 2022). Four ILs (IL005, IL017, IL035, and IL013) showed delayed flowering compared to Westar (P < 0.0001), and their reciprocal crosses displayed a phenotype intermediate in flowering time of both homozygote parents. These results indicated that flowering time is partial or incomplete dominance, and the flowering time locus mapped within a 1Mb region between two co-dominant polymorphic markers at 14.5-15.5Mb on chromosome A10. The flowering time locus was delineated to be between 14.60 and 15.5Mb based on genotypic data at the crossover site, and candidate genes within this region are associated with flowering time in canola and/or Arabidopsis. The co-dominant markers identified on chromosome A10 should be useful for marker assisted selection in breeding programs but will need to be validated to other breeding populations or germplasm accessions of canola.

A new leaf pubescence gene, Hl1th , introgressed into bread wheat from Thinopyrum ponticum and its phenotypic manifestation under homoeologous chromosomal substitutions.

Blue-grain lines were created on the basis of the spring bread wheat variety Saratovskaya 29 (S29) with chromosome 4B or 4D replaced with chromosome 4Th from Thinopyrum ponticum. The leaf pubescence of the two lines differs from S29 and from each other. In this work, we studied the effect of these substitutions on the manifestation of this trait. To quantify pubescence, the LHDetect2 program was used to determine trichome length and number on the leaf fold microphotographs. The key gene Hl1 on chromosome 4B and another unidentified gene with a weak effect determine the leaf pubescence of the recipient S29. Their interaction leads to the formation of trichomes of up to 300 microns in length. Replacement of both copies of chromosome 4B with two copies of wheatgrass chromosome 4Th modifies leaf pubescence in line S29_4Th(4B) so that the leaf pubescence characteristic of S29 becomes more sparse, and trichomes of up to 600- 700 μm in length are formed. Additionally, we described modification of pubescence in the substitution line S29_4Th(4D) where chromosome 4D that does not carry any pubescence gene was replaced. Under this substitution, trichomes of up to 400 μm in length were formed and the average length of trichomes on the underside of the leaf was reduced. The replacement of the Hl1 gene in the lines was also confirmed by the allelic state of the linked microsatellite marker Xgwm538. Thus, as a result of the studies, a new leaf pubescence gene introgressed from Th. ponticum into bread wheat was identified. We designated it as Hl1th. For the purpose of selection, we propose to use the unlicensed informative microsatellite markers Xgwm538 and Xgwm165, allowing chromosomes 4A, 4B, 4D and 4Th to be distinguished.

Exploring Novel Genomic Loci and Candidate Genes Associated with Plant Height in Bulgarian Bread Wheat via Multi-Model GWAS.

In the context of crop breeding, plant height (PH) plays a pivotal role in determining straw and grain yield. Although extensive research has explored the genetic control of PH in wheat, there remains an opportunity for further advancements by integrating genomics with growth-related phenomics. Our study utilizes the latest genome-wide association scan (GWAS) techniques to unravel the genetic basis of temporal variation in PH across 179 Bulgarian bread wheat accessions, including landraces, tall historical, and semi-dwarf modern varieties. A GWAS was performed with phenotypic data from three growing seasons, the calculated best linear unbiased estimators, and the leveraging genotypic information from the 25K Infinium iSelect array, using three statistical methods (MLM, FarmCPU, and BLINK). Twenty-five quantitative trait loci (QTL) associated with PH were identified across fourteen chromosomes, encompassing 21 environmentally stable quantitative trait nucleotides (QTNs), and four haplotype blocks. Certain loci (17) on chromosomes 1A, 1B, 1D, 2A, 2D, 3A, 3B, 4A, 5B, 5D, and 6A remain unlinked to any known Rht (Reduced height) genes, QTL, or GWAS loci associated with PH, and represent novel regions of potential breeding significance. Notably, these loci exhibit varying effects on PH, contribute significantly to natural variance, and are expressed during seedling to reproductive stages. The haplotype block on chromosome 6A contains five QTN loci associated with reduced height and two loci promoting height. This configuration suggests a substantial impact on natural variation and holds promise for accurate marker-assisted selection. The potentially novel genomic regions harbor putative candidate gene coding for glutamine synthetase, gibberellin 2-oxidase, auxin response factor, ethylene-responsive transcription factor, and nitric oxide synthase; cell cycle-related genes, encoding cyclin, regulator of chromosome condensation (RCC1) protein, katanin p60 ATPase-containing subunit, and expansins; genes implicated in stem mechanical strength and defense mechanisms, as well as gene regulators such as transcription factors and protein kinases. These findings enrich the pool of semi-dwarfing gene resources, providing the potential to further optimize PH, improve lodging resistance, and achieve higher grain yields in bread wheat.

Introgression of Thrips Resistance from Pima Cotton (Gossypium barbadense L.) into Upland Cotton (Gossypium hirsutum L.)

Thrips are major early season insect pests that cause significant economic damage in Upland cotton in the U.S. Development and deployment of resistant cultivars is the most effective and ecologically sustainable means of reducing thrips damage in cotton. Interspecific hybridization and backcrossing were performed to introgress thrips resistance from Pima cotton (Gossypium barbadense L.) accession Coastland 320 into Upland cotton (Gossypium hirsutum L.) cultivars Acala Maxxa (AM) and Fiber Max 966 (FM966). Backcross populations were screened for thrips resistance in thrips screening summer field nurseries in North Carolina. Thirty-two BC2F2 plants with thrips resistance were identified and backcrossed further to develop BC3F2 plants. Eleven AM derived BC2F2 resistant plants and 21 FM966 derived BC2F2 resistant plants were genotyped using CottonSNP63K array to identify the Pima chromatin in the introgression lines (ILs). In the ILs, introgressed Pima chromatin was detected on chromosomes A01, A08, A09, A10, A11, D10, D11, D12, and D13. Of these, four ILs, two each in AM and FM966 background, showed overlapped introgressed Pima chromatin on chromosomes A10 and D11. Further, four introgression lines, two each in AM and FM966 background, shared a common Pima introgression on chromosome D13. Characterization of thrips species in the screening nursery showed that predominant thrips species were tobacco thrips (Frankliniella fusca (Hinds)) followed by western flower thrips (Frankliniella occidentalis (Pergande)). The identified ILs with thrips resistance should be a useful source of genetic variability for developing Upland cotton cultivars with pest resistance.

Genetic dissection and genomic prediction of drought indices in bread wheat (Triticum aestivum L.) genotypes.

Drought constitutes the main obstacle to agricultural productivity in the Central and West Asia and North Africa (CWANA) region, notably leading to substantial reductions in wheat yields due to terminal water stress. The adoption of drought-resistant wheat varieties appears to be a vital strategy to maintain wheat production in the face of climatic challenges. In this context, a study was conducted utilizing a set of 198 elite bread wheat genotypes developed at the International Center for Agricultural Research in the Dry Areas (ICARDA). This set of elite genotypes was evaluated at the Sidi Al-Aidi station in Morocco over two years (2021-2022), under rain-fed and irrigated conditions. Phenotypic assessments for grain yield and drought indices were performed, alongside genotyping the population using 15k SNP markers. These preparatory steps facilitated a genome-wide association study (GWAS) and genomic prediction, leveraging the Mixed Linear Model (MLM) to pinpoint marker-trait associations (MTAs) and candidate genes pertinent to grain yield and drought indices. The results manifested substantial variations in both grain yield and drought indices among the genotypes tested. Grain yield performance ranged from 0.34 to 2.57 t/ha under rain-fed conditions and 1.12 to 4.57 t/ha under irrigated scenarios. The comprehensive analysis identified 39 significant MTAs (p < 0.001) and 14 putative genes associated with drought indices and grain yield. Noteworthy is the marker “wsnp_Ex_c12127_19394952” on chromosome 5B, which displayed a significant correlation with grain yield in rain-fed environments. Furthermore, the most prominent marker linked to tolerance index (TOL) was “BobWhite_c42349_99”, situated on chromosome 5A and associated with the TraesCS5A02G498000 gene. This gene plays a critical role, encoding for catalase protein crucial for response to hydrogen peroxide. These markers could be used for marker-assisted selection in wheat breeding programs targeting drought tolerance.

Identification of Genomic Regions Conferring Enhanced Zn and Fe Concentration in Wheat Varieties and Introgression Lines Derived from Wild Relatives.

Wild and cultivated relatives of wheat are an important source of genetic factors for improving the mineral composition of wheat. In this work, a wheat panel consisting of modern bread wheat varieties, landraces, and introgression lines with genetic material of the wheat species Triticum timopheevii, T. durum, T. dicoccum, and T. dicoccoides and the synthetic line T. kiharae was used to identify loci associated with the grain zinc (GZnC) and iron (GFeC) content. Using a BLINK model, we identified 31 and 73 marker-trait associations (MTAs) for GZnC and GFeC, respectively, of which 19 were novel. Twelve MTAs distributed on chromosomes 1B, 2A, 2B, 5A, and 5B were significantly associated with GZnC, five MTAs on 2A, 2B, and 5D chromosomes were significantly associated with GFeC, and two SNPs located on 2A and 2B were related to the grain concentration of both trace elements. Meanwhile, most of these MTAs were inherited from At and G genomes of T. timopheevii and T. kiharae and positively affected GZnC and GFeC. Eight genes related to iron or zinc transporters, representing diverse gene families, were proposed as the best candidates. Our findings provide an understanding of the genetic basis of grain Zn and Fe accumulation in species of the Timopheevi group and could help in selecting new genotypes containing valuable loci.

Genome-wide association study and KASP marker development for starch quality traits in wheat.

Starch is the main component of wheat (Triticum aestivum L.) flour, and its quality directly affects the processing quality of the final product. To investigate the genetic basis of starch, this study assessed the starch quality traits of 341 winter wheat varieties/lines grown in Emin and Qitai during the years 2019-2020 and 2020-2021. A genome-wide association study was conducted with the genotype data obtained from wheat 40K breeding chips using the mixed linear model. Wheat starch quality traits exhibited coefficients of variation ranging from 1.43% to 23.66% and broad-sense heritabilities between 0.37 and 0.87. All traits followed an approximately normal distribution, except for T. There were highly significant correlations among starch quality traits, with the strongest correlation observed between final viscosity (FV) and trough viscosity (TV) (r=0.748), followed by peak viscosity and breakdown (BD) (r=0.679). Thirty-four single-nucleotide polymorphism markers significantly and stably associated with starch quality traits were identified, clustering in 31 genetic loci. These included one locus for TV, six loci for BD, three loci for FV, two loci for peak time (PT), 12 loci for T, five loci for falling number, and two loci for damaged starch. One PT-related block of 410kb was identified in the region of 596 Mb on chromosome 5A, where significant phenotypic differences were observed between different haplotypes. One Kompetitive allele-specific PCR (KASP) marker for T was developed on chromosome 7B, and two KASP markers for BD were developed on chromosome 7A. Four candidate genes possibly affecting BD during grain development were identified on chromosome 7A, including TraesCS7A02G225100.1, TraesCS7A02G225900.1, TraesCS7A02G226400.1, and TraesCS7A02G257100.1. The results have significant implications for utilizing marker-assisted selection in breeding to improve wheat starch quality.

Genetic Mapping and Characterization of the Clubroot Resistance Gene BraPb8.3 in Brassica rapa.

Clubroot, a significant soil-borne disease, severely impacts the productivity of cruciferous crops. The identification and development of clubroot resistance (CR) genes are crucial for mitigating this disease. This study investigated the genetic inheritance of clubroot resistance within an F2 progeny derived from the cross of a resistant parent, designated "377", and a susceptible parent, designated "12A". Notably, "377" exhibited robust resistance to the "KEL-23" strain of Plasmodiophora brassicae, the causative agent of clubroot. Genetic analyses suggested that the observed resistance is controlled by a single dominant gene. Through Bulked Segregant Analysis sequencing (BSA-seq) and preliminary gene mapping, we localized the CR gene locus, designated as BraPb8.3, to a 1.30 Mb genomic segment on chromosome A08, flanked by the markers "333" and "sau332-1". Further fine mapping precisely narrowed down the position of BraPb8.3 to a 173.8 kb region between the markers "srt8-65" and "srt8-25", where we identified 22 genes, including Bra020861 with a TIR-NBS-LRR domain and Bra020876 with an LRR domain. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses confirmed that both Bra020861 and Bra020876 exhibit increased expression levels in the resistant parent "377" following inoculation with P. brassicae, thereby underscoring their potential as key genes implicated in BraPb8.3-mediated clubroot resistance. This study not only identifies molecular markers associated with BraPb8.3 but also enriches the genetic resources available for breeding programs aimed at enhancing resistance to clubroot.

Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data.

Wheat, particularly common wheat (Triticum aestivum L.), is a major crop accounting for 25% of the world cereal production and thriving indiverse ecogeographic regions. Its adaptation to diverse environments arises from its three distinct genomes adapted to different environments and post-domestication anthropogenic interventions. In search of key genomic regions revealing historic events and breeding significance to common wheat, we performed genome scan and genome-environment association (GEA) analyses using high-marker density genotype datasets. Whole-genome scans revealed highly differentiated regions on chromosomes 2A, 3B, and 4A. In-depth analyses corroborated our previous prediction of the 4A differentiated region signifying the separation between Spelt/Macha and other wheat types. Individual chromosome scans captured key introgressions, includingone from T. timopheevii and one fromThinopyrum ponticum on 2B and 3D, respectively, as well as known genes such as Vrn-A1 on 5A. GEA highlighted loci linked to latitude-induced environmental variations, influencing traits such as photoperiodism and responses to abiotic stress. Variation at theVrn-A1 locus on 5A assigned accessions to two haplotypes (6% and 94%). Further analysis on Vrn-A1 coding gene revealed four subgroups of the major haplotype, while the minor haplotype remained undifferentiated. Analyses at differentiated loci mostly dichotomized the population, illustrating the possibility of isolating pre-breeding materials with desirable traits from large gene pools in the absence of phenotype data. Given the current availability of broad genetic data, the genome-scan-GEA hybrid can be anefficient and cost-effective approach for pinpointing environmentally resilient pre-breeding germplasm from vast gene pools, including gene banks regardless of trait characterization.