Cauliflower is a distinct subspecies of the Brassica oleracea plants due to its specialized and edible floral organ. Cauliflower curd is composed of enlarged inflorescence meristems that developed by a series of precise molecular regulations. Based solely on the curd solidity, cauliflower is generally classified into two groups (compact-curd and loose-curd), where curd branch length acts as a crucial parameter to determine the curd morphological difference. Herein, to understand the genetic basis of curd branch development, we utilized a total of 298 inbred lines representing two groups of cauliflower to comprehensively investigate the causal genes and regulatory mechanisms. Phylogenetic and population structure analyses revealed that two subgroups could be further categorized into the compact-curd and the loose-curd groups, respectively. Integrating the genotype and phenotype data, we conducted a genome-wide association study for the length of the outermost branch (LOB) and secondary branch (LSB) of the curd. Sixty-four significant loci were identified that are highly associated with curd branch development. Evidence from genome-wide selective sweep analysis (FST and XP-EHH) narrowed down the major signal on chromosome 8 into an approximately 79 kb region which encodes eleven protein-coding genes. After further analysis of haplotypes, transcriptome profiling, and gene expression validation, we finally inferred that BOB08G028680, as a homologous counterpart of AtARR9, might be the causal gene for simultaneously regulating LOB and LSB traits in cauliflower. This result provides valuable information for improving curd solidity in future cauliflower breeding.
As important secondary metabolites in plants, anthocyanins not only contribute to colored plants organs, but also provide protections against various biotic and abiotic stresses. In this study, a MYB transcription factor gene TdRCA1 from wild emmer wheat regulating anthocyanin biosynthesis in wheat coleoptile was identified on the short arm of chromosome 7A in common wheat genetic background. The TdRCA1 overexpression lines showed colored callus, coleoptile, auricle and stem nodes, as well as up regulation of six anthocyanin-related structural genes. The expression of TdRCA1 was activated by light in a temporal manner. While coleoptile color of 48 and 60 h dark-grown seedlings changed from green to red after 24 h light treatment, those grown in dark for 72 and 96 h failed to develop red coleoptiles after light restoration. Interestingly, the over expression of TdRCA1 resulted in increased resistance to Fusarium crown rot, a chronic and severe fungal disease in many cereal growing regions in the world. Our results offer a better understanding of the molecular basis of coleoptile color in bread wheat.
Key message: Two genomic regions associated with FFBN and HFFBN and a potential regulatory gene (GhE6) of HFFBN were identified through the integration of RTM-GWAS and meta‑QTL analyses. Abstract The first fruit branch node (FFBN) and the height of the first fruit branch node (HFFBN) are two important traits that are related to plant architecture and early maturation in upland cotton. Several studies have been conducted to elucidate the genetic basis of these traits in cotton using biparental and natural populations. In this study, by using 9,244 SNP linkage disequilibrium block (SNPLDB) loci from 315 upland cotton accessions, we carried out restricted two-stage multilocus and multiallele genome-wide association studies (RTM-GWASs) and identified promising haplotypes/alleles of the four stable and true major SNPLDB loci that were significantly associated with FFBN and HFFBN. Additionally, a meta-quantitative trait locus (MQTL) analysis was conducted on 274 original QTLs that were reported in 27 studies, and 40 MQTLs associated with FFBN and HFFBN were identified. Through the integration of the RTM-GWAS and meta‑QTL analyses, two stable and true major SNPLDBs (LDB_5_15144433 and LDB_16_37952328) that were distributed in the two MQTLs were identified. Ultimately, 142 genes in the two genomic regions were annotated, and three candidate genes associated with FFBN and HFFBN were identified in the genomic region (A05:14.64-15.64 Mb) via RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6 was a key gene related to HFFBN and that GhDRM1 and GhGES were important genes associated with early flowering in upland cotton. These findings will aid in the future identification of molecular markers and genetic resources for developing elite early-maturing cultivars with ideal plant characteristics.
The Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D. Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.
Key message: Five QTL for wheat grain protein content were identified, and the effects of two dwarfing genes Rht-B1b and Rht-D1b on grain protein content were validated in multiple populations. Grain protein content (GPC) plays an important role in wheat quality. Here, a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) for GPC. Two hundred and five RILs and their parents were grown in three years in randomized complete blocks each with two replications, and genotyped using the wheat 55 K SNP array. Five QTL were identified for GPC on chromosomes 1A, 1B, 2D, 4B, and 4D. Notably, QGpc.yaas-4B (co-located with Rht-B1) and QGpc.yaas-4D (co-located with Rht-D1) were consistently detected across all experiments and best linear unbiased estimating, accounting for 6.61-8.39% and 6.05-10.21% of the phenotypic variances, respectively. The effects of these two dwarfing alleles Rht-B1b and Rht-D1b on reducing GPC and plant height were validated in two additional RIL populations and one natural population. This study lays a foundation for further investigating the effects of dwarfing genes Rht-B1b and Rht-D1b on wheat GPC.
Key message: Multi-environmental characterization of flag leaf morphology traits in the US winter wheat revealed nine stable genomic regions for different flag leaf-related traits including a major region governing flag leaf angle. Flag leaf in wheat is the primary contributor to accumulating photosynthetic assimilates. Flag leaf morphology (FLM) traits determine the overall canopy structure and capacity to intercept the light, thus influencing photosynthetic efficiency. Hence, understanding the genetic control of these traits could be useful for breeding desirable ideotypes in wheat. We used a panel of 272 accessions from the hard winter wheat (HWW) region of the USA to investigate the genetic architecture of five FLM traits including flag leaf length (FLL), width (FLW), angle (FLANG), length-width ratio, and area using multilocation field experiments. Multi-environment GWAS using 14,537 single-nucleotide polymorphisms identified 36 marker-trait associations for different traits, with nine being stable across environments. A novel and major stable region for FLANG (qFLANG.1A) was identified on chromosome 1A accounting for 9-13% variation. Analysis of spatial distribution for qFLANG.1A in a set of 2354 breeding lines from the HWW region showed a higher frequency of allele associated with narrow leaf angle. A KASP assay was developed for allelic discrimination of qFLANG.1A and was used for its independent validation in a diverse set of spring wheat accessions. Furthermore, candidate gene analysis for two regions associated with FLANG identified seven putative genes of interest for each of the two regions. The present study enhances our understanding of the genetic control of FLM in wheat, particularly FLANG, and these results will be useful for dissecting the genes underlying canopy architecture in wheat facilitating the development of climate-resilient wheat varieties.
Key message: Pigmentation changes in canopy leaves were first reported, and subsequent genetic analyses identified a major QTL associated with levels of pigmentation changes, suggesting Glyma.06G202300 as a candidate gene. An unexpected reddish-purple pigmentation in upper canopy leaves was discovered during the late reproductive stages in soybean (Glycine max L.) genotypes. Two sensitive genotypes, 'Uram' and PI 96983, exhibited anomalous canopy leaf pigmentation changes (CLPC), while 'Daepung' did not. The objectives of this study were to: (i) characterize the physiological features of pigmented canopy leaves compared with non-pigmented leaves, (ii) evaluate phenotypic variation in a combined recombinant inbred line (RIL) population (N = 169 RILs) under field conditions, and (iii) genetically identify quantitative trait loci (QTL) for CLPC via joint population linkage analysis. Comparison between pigmented and normal leaves revealed different Fv/Fm of photosystem II, hyperspectral reflectance, and cellular properties, suggesting the pigmentation changes occur in response to an undefined abiotic stress. A highly significant QTL was identified on chromosome 6, explaining ~ 62.8% of phenotypic variance. Based on the QTL result, Glyma.06G202300 encoding flavonoid 3'-hydroxylase (F3'H) was identified as a candidate gene. In both Uram and PI 96983, a 1-bp deletion was confirmed in the third exon of Glyma.06G202300 that results in a premature stop codon in both Uram and PI 96983 and a truncated F3'H protein lacking important domains. Additionally, gene expression analyses uncovered significant differences between pigmented and non-pigmented leaves. This is the first report of a novel symptom and an associated major QTL. These results will provide soybean geneticists and breeders with valuable knowledge regarding physiological changes that may affect soybean production. Further studies are required to elucidate the causal environmental stress and the underlying molecular mechanisms.
The common wheat line 4N0461 showed adult-plant resistance to leaf rust. 4N0461 was crossed with susceptible cultivars Nongda4503 and Shi4185 to map the causal resistance gene(s). Segregation of leaf rust response in F2 populations from both crosses was 9 resistant:7 susceptible, indicative of two complementary dominant resistance genes. The genes were located on chromosome arms 3BS and 4BL and temporarily named LrN3B and LrN4B, respectively. Subpopulations from 4N0461 × Nongda4503 with LrN3B segregating as a single allele were used to fine-map LrN3B locus. LrN3B was delineated in a genetic interval of 0.07 cM, corresponding to 106 kb based on the Chinese Spring reference genome (IWGSC RefSeq v1.1). Four genes were annotated in this region, among which TraesCS3B02G014800 and TraesCS3B02G014900 differed between resistant and susceptible genotypes, and both were required for LrN3B resistance in virus-induced gene silencing experiments. Diagnostic markers developed for checking the polymorphism of each candidate gene, can be used for marker-assisted selection in wheat breeding programs.
Key message: Developing genetically resistant soybean cultivars is key in controlling the destructive Sclerotinia Stem Rot (SSR) disease. Here, a GWAS study in Canadian soybeans identified potential marker-trait associations and candidate genes, paving the way for more efficient breeding methods for SSR. Sclerotinia stem rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is one of the most important diseases leading to significant soybean yield losses in Canada and worldwide. Developing soybean cultivars that are genetically resistant to the disease is the most inexpensive and reliable method to control the disease. However, breeding for resistance is hampered by the highly complex nature of genetic resistance to SSR in soybean. This study sought to understand the genetic basis underlying SSR resistance particularly in soybean grown in Canada. Consequently, a panel of 193 genotypes was assembled based on maturity group and genetic diversity as representative of Canadian soybean cultivars. Plants were inoculated and screened for SSR resistance in controlled environments, where variation for SSR phenotypic response was observed. The panel was also genotyped via genotyping-by-sequencing and the resulting genotypic data were imputed using BEAGLE v5 leading to a catalogue of 417 K SNPs. Through genome-wide association analyses (GWAS) using FarmCPU method with threshold of FDR-adjusted p-values < 0.1, we identified significant SNPs on chromosomes 2 and 9 with allele effects of 16.1 and 14.3, respectively. Further analysis identified three potential candidate genes linked to SSR disease resistance within a 100 Kb window surrounding each of the peak SNPs. Our results will be important in developing molecular markers that can speed up the breeding for SSR resistance in Canadian grown soybean.
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