Black rice gains recognition in functional food and nutraceutical for its secondary metabolite profiles, which exhibit antioxidant, anti-diabetic, anti-hyperlipidaemic, and anti-cancer properties. Its unique purple-black colour trait results from anthocyanin accumulation in the pericarp, a trait that varies across pigmented genotypes. While the genetic basis of grain pigmentation in black rice has been partially elucidated, the influence of environmental factors, particularly ultraviolet (UV) radiation, remains poorly understood. UVB radiation is thought to play a role in regulating anthocyanin regulation in various crops, suggesting a potential advantage for cultivating black rice in high UV regions. This research aimed to identify quantitative trait loci (QTL) linking grain pigmentations in response to UV exposure. A genome-wide association study (GWAS) was performed on a diversity panel of 191 black rice accessions primarily sourced from the Asia-Pacific region. Utilising 31,501 single-nucleotide polymorphisms (SNPs), GWAS revealed distinct associations for anthocyanin content under UV conditions versus under non-UV conditions. Notably, three candidate genes associated with anthocyanin biosynthesis under UV exposure were identified: OsBBX14 , known to activate OsC1 or OsB2 in anthocyanin biosynthesis pathway; OsMYB44 , a transcription factor that promotes UV-B tolerance; and OsbZIP71 , which improves abiotic stress tolerance by reducing reactive oxygen species (ROS) accumulation. These findings provide critical insights into the genotype-by-environment interactions of grain pigmentation traits and pinpoint potential candidate genes for further validation and molecular marker development. Ultimately, this research supports the development of black rice varieties with enhanced nutritional value and improved resilience to high-UV growing conditions.

Cannabis sativa L. has been cultivated for millennia as a source of food and fibre. Increasing demand for functional foods has renewed interest in C. sativa seeds (hempseeds), which are rich in essential fatty acids and amino acids. However, a near-global moratorium on C. sativa cultivation and research throughout most of the 20th century has delayed crop improvement using modern breeding approaches. As a result, genetic loci contributing to key agronomic traits, including with respect to maximizing yield as a seed crop, remain largely unknown. In this study, a feminized segregating F2 mapping population, derived from a tall parent with spacious inflorescences and large seeds and a short-stature parent with compact inflorescences and small seeds, was phenotyped for key seed and agronomic traits related to yield. A mid-density Single Nucleotide Polymorphism (SNP) genotyping panel was used to generate a genetic linkage map of 291.5 cM with 455 SNPs. Quantitative Trait Locus (QTL) mapping identified major loci for hundred-seed weight—qHSW3, 26.59 percent variance explained (PVE), seed volume—qSV1, 33.24 PVE, and plant height—qPH9, 46.99 PVE. Our results provide novel target regions, associated molecular markers, and candidate genes for future breeding efforts to improve C. sativa.

A new stripe rust resistance gene YrAn1589 in Chinese wheat Annong1589 was mapped to a 160.9-166.6 kb interval on chromosome arm 3BL and co-segregated with a marker CAPS9 developed from candidate gene TraesCS3B03G1054600. Stripe rust, caused by Puccinia. striiformis f. sp. tritici (Pst), is a devastating fungal disease that can significantly reduce wheat yield. The Chinese wheat cultivar Annong1589 demonstrates high resistance against the predominant Pst races in the Huang-Huai valley wheat region. The present study aimed to identify the stripe rust resistance gene in Annong1589. Genetic analysis indicated that the resistance in Annong1589 was conferred by a single dominant gene, provisionally designated YrAn1589. Using Wheat660K SNP array, bulked segregant RNA sequencing and new molecular markers developed, the resistance gene was mapped to a 160.9–166.6 kb region between CAPS8 and CAPS10 on chromosome 3BL based on IWGSC CS RefSeq v2.1 and eight other reference genome sequences, including eight high-confidence annotated genes. Transcriptome and qRT-PCR analyses revealed significantly upregulated expression of TraesCS3B03G1054600 in resistant plants following CYR32 inoculation, suggesting it is a potential candidate gene for YrAn1589. A functional marker CAPS9 developed from a A/G polymorphic SNP in the candidate co-segregated with YrAn1589 in the F2 population. Subcellular localization experiments showed that TraesCS3B03G1054600 protein was localized in the cytoplasm and nucleus, implying its role in immune response and resistance. Our findings establish YrAn1589 as a new stripe rust resistance gene, providing valuable gene resource and molecular markers for improvement of stripe rust resistance in wheat.

Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97

In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.

Glucosinolates (GSLs) are sulphur- and nitrogen-containing secondary metabolites implicated in the fitness of Brassicaceae and appreciated for their pungency and health-conferring properties. In Indian mustard (Brassica juncea L.), GSL content and composition are seed-quality-determining traits affecting its economic value. Depending on the end use, i.e., condiment or oil, different GSL levels constitute breeding targets. The genetic control of GSL accumulation in Indian mustard, however, is poorly understood, and current knowledge of GSL biosynthesis and regulation is largely based on Arabidopsis thaliana. A genome-wide association study was carried out to dissect the genetic architecture of total GSL content and the content of two major GSLs, sinigrin and gluconapin, in a diverse panel of 158 Indian mustard lines, which broadly grouped into a South Asia cluster and outside-South-Asia cluster. Using 14,125 single-nucleotide polymorphisms (SNPs) as genotyping input, seven distinct significant associations were discovered for total GSL content, eight associations for sinigrin content and 19 for gluconapin. Close homologues of known GSL structural and regulatory genes were identified as candidate genes in proximity to peak SNPs. Our results provide a comprehensive map of the genetic control of GLS biosynthesis in Indian mustard, including priority targets for further investigation and molecular marker development.

Glucosinolates (GSLs) are secondary metabolites produced by members of the genus Brassica. These compounds impart the pungency to brassica vegetables and oils. Due to their health benefits, which include anti-cancer and anti-fungal properties, they have been attracting interest in research. Indian mustard (B. juncea L.), used as condiment and oil crop has high natural levels of seed glucosinolates and displays exploitable natural variation in this trait. In this study a diverse collection of 161 mustard lines originating from 21 countries, will be genotyped and phenotyped. Traits of interest include seed GSLs (sinigrin, gluconapin, progroitin, epi-progoitin and glucoiberin), oil and protein content, as well as basic agro-morphological performance such as height, flowering time and yield. Current knowledge on GSL biosynthesis and its genetic regulation mostly relies on data from Arabidopsis thaliana. We aim to elucidate the genetic architecture of GSL content and composition in relation to other seed traits (oil and protein content) in our diversity panel through association mapping. Additionally, we are aiming to resolve genome complexity of GSL genes in mustard genome in contrast to A. thaliana by identifying gene copy number through in silico analysis. Outcome of this study will help streamline the breeding and product development for either high GSL mustard lines for condiment use or low GSL lines for canola-type oil use. Our preliminary data on seed GSLs seems to reflect the historical use of mustard in different geographical regions. Chinese and European lines featured higher GSL while lines from the Indian subcontinent displayed lower GSL contents.

Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers’ nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7–8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost–benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.

BackgroundWhile a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs.ResultsEmpirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications.ConclusionsThis study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.

BACKGROUND:A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding.RESULTS:A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes.CONCLUSIONS:The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in improving and diversifying resistance to BB.

Significant GWAS SNP hits that are flanking/overlapping with known resistance genes for bacterial blight. (XLSX 92 kb)