Seed Coat Color Research Articles

Phenotypic characterization of different seed coat color of cowpea cultivars, Vigna unguiculata (L). Walp. in West-Central Côte d'Ivoire

Cowpea is a widely consumed legume in sub-Saharan Africa. Several cowpea cultivars based on seed coat color are widely observed. Consumers' choice of cultivar varies from one region to another. However, the lack of improved varieties and the limited availability of information on the productive potential of these cultivars is one of the constraints on the development of cowpea production. Thus, red, white, black and brown seed coat widely consumed were evaluated in the field over two consecutive years, 2022 and 2023 on a plot following a randomized complete block design with four replications. Morphological and agronomic parameters showed that there were two groups of cultivars with interesting agronomic characteristics. The first group composed of the black, brown and red cultivars had a relatively short reproductive time, averaging 66 days. These cultivars are considered early. The number of fruits of these cultivars was also high, with an average of 12 fruits per plant. The second group, consisting exclusively of the white seed coat cultivar produced high biomass and plant length. It had also twice the pod and seed weight of the other cultivars. It would be possible to develop hybrids in the future, seeking, for example, to improve the seed weight of the red cultivar with a short reproductive cycle by crossing with the white seed coat cultivar, with a view to creating an early variety with a high yield.

Relationship between seed coat colour and seed vigour in cowpea (Vigna unguiculata Walp (L.)

In the present study, the 25 genotypes were grouped into two seed color groups including pigmented (n = 19; black, brown, dark brown, grey, dark grey seed color) and unpigmented (n = 6; cream and white seed color) for studying the association of seed coat color with seed vigor. Despite high germination (>84%) of all genotypes in the laboratory, unpigmented genotypes recorded low (34-54%) field emergence than pigmented genotypes (52-78%). Rapid initial (30 min) rate of water uptake (-0.75**), water uptake at one hour of imbibition (-0.70**), low proportion of seed coat (0.67**), and greater electrical conductivity of seed leachate (-0.72**) was associated with low field emergence in unpigmented cowpea genotypes. No significant correlation or association was observed between field emergence and laboratory germination in the present investigation suggesting that laboratory germination can not be used for predicting field emergence in cowpea. Instead, the electrical conductivity of seed leachate could be used to predict the field emergence of cowpea.

Identification of lncRNAs regulating seed traits in Brassica juncea and development of a comprehensive seed omics database.

Brassica juncea is a crucial oilseed crop, and its seeds possess high economic value as they are a source of edible oil. In order to understand the role of long non coding RNAs (lncRNAs) in the regulation of seed development, we carried out computational analysis using transcriptome data of developing seeds of two contrasting genotypes of B. juncea, Pusajaikisan (PJK) and Early Heera 2 (EH2). The seeds were sampled at three stages, 15, 30, and 45 days after pollination. We identified 1,539 lncRNAs, of which 809 were differentially expressed. We also carried out extensive characterization and functional analysis of seed lncRNAome. The expression patterns were analysed using k-means clustering, and the targets were analysed using pathway, transcription factor, and GO enrichment, as well as ortholog information. We shortlisted a total of 25 robust lncRNA candidates for seed size, oil content, and seed coat color. We also identified 4 lncRNAs as putative precursors of miRNAs regulating seed development. Moreover, a total of 28 miRNA-lncRNA-mRNA regulatory networks regulating seed traits were identified. We also developed a comprehensive database, (BrassIca juncea database or "BIJ" ( https://bij.cuh.ac.in/ ), which provides seed omics as well as other functional genomics and genetics data in an easily accessible form. These candidate lncRNAs are suitable for including in crop improvement programs through molecular breeding, as well as for future validations through genome editing. Together, the knowledge of these candidate lncRNAs and availability of BIJ database shall leverage the crop improvement efforts in B. juncea.

Seed traits inheritance in Fagopyrum esculentum Moench. based on image analysis method.

Common buckwheat (Fagopyrum esculentum Moench.) is one of the most important orphan crops worldwide. Various research efforts have been done to improve cultivation methods to enhance important agronomic traits such as productivity and biotic/abiotic resistance. One important aspect is the seed trait, which has not been extensively studied due to the time-consuming and tedious nature of its examination. Despite this, understanding seed traits is crucial for meeting consumer needs and optimizing crop yields. Therefore, the aim of the study is to investigate the inheritance of common buckwheat seed traits-such as shape, size, and coat color-using an image-based approach. This method allows for the analysis of a large number of seeds with a level of accuracy and precision that was previously unattainable. The results indicate that seed coat color is inherited maternally. Notably, the parameters in size had substantial increases acting like overdominance. The number of seeds that were harvested from F1s of each cross differed a lot depending on the cross combinations and pin/thrum type. In addition, seed size had large reduction in F1s from the different seed-sized parents, especially in thrum type. These may show that there could be cross barriers. The results revealed trends of maternal inheritance for seed shape and coat color in buckwheat, an area that has not been extensively studied. These findings could support buckwheat breeding efforts, helping to address market needs and food demands in the face of significant climate change.

High-density genetic map construction and QTL mapping to identify genes for blight defense- and yield-related traits in sesame (Sesamum indicum L.).

Sesame (Sesamum indicum L.) is an important oilseed crop widely cultivated in subtropical and tropical areas. Low genetic yield potential and susceptibility to disease contribute to low productivity in sesame. However, the genetic basis of sesame yield- and disease-related traits remains unclear. Here, we represent the construction of a high-density bin map of sesame using whole genome sequencing of an F2 population derived from 'Yizhi' and 'Mingdeng Zhima'. A total of 2766 Bins were categorized into 13 linkage groups. Thirteen significant QTLs were identified, including ten QTLs related to yield, two QTLs related to Sesame Fusarium wilt (SFW) disease, and one QTL related to seed color. Among these QTLs, we found that SFW-QTL1.1 and SFW-QTL1.2 were major QTLs related to Fusarium wilt disease, explaining more than 20% of the phenotypic variation with LOD > 6. SCC-QTL1.1 was related to seed coat color, explaining 52% of the phenotypic variation with LOD equal to 25.3. This suggests that seed color traits were controlled by a major QTL. Candidate genes related to Fusarium wilt disease and seed color in the QTLs were annotated. We discovered a significant enrichment of genes associated with resistance to late blight. These genes could be spectral disease resistance genes and may have a role in the regulation of Fusarium wilt disease resistance. Our study will benefit the implementation of marker-assisted selection (MAS) for the genetic improvement of disease resistance and yield-related traits in sesame.

Genome-Wide Identification of B-Box Family Genes and Their Potential Roles in Seed Development under Shading Conditions in Rapeseed.

B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development.

Association Mapping of Seed Coat Color Characteristics for Near-Isogenic Lines of Colored Waxy Maize Using Simple Sequence Repeat Markers.

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of "Mibaek 2ho" variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the "Mibaek 2ho" variety waxy maize.

Computer vision for assessment the seed coat color of carioca common beans

AbstractConsumer acceptance of common beans (Phaseolus vulgaris L.) belonging to the Carioca commercial group depends on the color of the seed. Therefore, producers seek bean cultivars that have a light seed coat after storage. This trait is very important for common bean breeding programs dedicated to produce a high market demand. Therefore, the objective was to propose and assess the use of a computer vision‐based methodology for assessing common bean color at harvest and after storage. A total of 70 carioca bean cultivars were visually assessed using a grading scale and computer vision after harvest and 90 days after the first assessment. The images allowed the cultivars to be discriminated according to the seed coat color. The accuracies with both assessment methodologies were >0.90. In addition, the correlations between these methodologies were ≤−0.72. The coefficients of variation for computer vision were lower than 6.50, while for the visual assessment, they were >10.08. Therefore, computer vision applied to assess the seed coat color of carioca bean grains is precise and accurate and allows for better discrimination than the visual assessment. Therefore, image analysis will assist in selecting better cultivars in breeding programs.

CaLAP1 and CaLAP2 orchestrate anthocyanin biosynthesis in the seed coat of Cicer arietinum.

Our findings shed light on the regulation of anthocyanin and proanthocyanidin biosynthesis in chickpea seed coats. Expression of R2R3-MYB transcription factors CaLAP1 and CaLAP2 enhanced the anthocyanins and proanthocyanidins content in chickpea. The seed coat color is a major economic trait in leguminous crop chickpea (Cicer arietinum). Anthocyanins and proanthocyanidins (PAs) are two classes of flavonoids that mainly contribute to the flower, seed coat and color of Desi chickpea cultivars. Throughout the land plant lineage, the accumulation of anthocyanins and PAs is regulated by MYB and bHLH transcription factors (TFs), which form an MBW (MYB, bHLH, and WD40) complex. Here, we report two R2R3-MYB TFs in chickpea belonging to the anthocyanin-specific subgroup-6, CaLAP1 (Legume Anthocyanin Production 1), and CaLAP2 (Legume Anthocyanin Production 2), which are mainly expressed in the flowers and developmental stages of the seeds. CaLAP1 and CaLAP2 interact with TT8-like CabHLH1 and WD40, forming the MBW complex, and bind to the promoter sequences of anthocyanin- and PA biosynthetic genes CaCHS6, CaDFR2, CaANS, and CaANR, leading to anthocyanins and PA accumulation in the seed coat of chickpea. Moreover, these CaLAPs partially complement the anthocyanin-deficient phenotype in the Arabidopsis thaliana sextuple mutant seedlings. Overexpression of CaLAPs in chickpea resulted in significantly higher expression of anthocyanin and PA biosynthetic genes leading to a darker seed coat color with higher accumulation of anthocyanin and PA. Our findings show that CaLAPs positively modulate anthocyanin and PA content in seed coats, which might influence plant development and resistance to various biotic and abiotic stresses.

Effect of Origin, Seed Coat Color, and Maturity Group on Seed Isoflavones in Diverse Soybean Germplasm.

Soybeans are grown worldwide owing to their protein, oil, and beneficial bioactive compounds. Genetic and environmental factors influence soybean seed isoflavones. In the present study, we profiled the seed isoflavones in world diverse soybean germplasm grown in two locations over two years in China. Significant differences (p < 0.001) were observed between the accessions, accession origins, seed coat colors, and maturity groups for individual and total isoflavone (TIF) content. TIF content of the soybean accessions ranged from 677.25 μg g-1 to 5823.29 μg g-1, representing an 8-fold difference. USA soybean accessions showed the highest mean TIF content (3263.07 μg g-1), followed by Japan (2521.26 μg g-1). Soybean with black seed coat showed the highest (3236.08 μg g-1) TIF concentration. Furthermore, isoflavone levels were significantly higher in late-maturity groups. Correlation analysis revealed significant positive associations between individual and TIF content. Malonyldaidzin and malonylgenistin showed higher correlations with TIF content (r = 0.92 and r = 0.94, respectively). The soybean accessions identified as having high and stable TIF content can be utilized in the food and pharmaceutical industries and breeding programs to develop soybean varieties with enhanced isoflavone content.

Growth and production of M6 and M7 black soybean mutant genotypes

Abstract. Anwar S, Kusmiyati F, Lukiwati DR, Sas MGA, Arifah YN. 2024. Growth and production of M6 and M7 black soybean mutant genotypes. Biodiversitas 25: 2541-2546. The seed coat colors of soybeans are yellow, black, green, brown, or bicolor, and in Indonesia, black seed coat color is for used soy sauce. Our black soybean mutation breeding research started with irradiating soybean cultivar Detam 3 with gamma rays at 160, 208, 256, 304, 352, 400, 448, 496, 544, and 592 Gy. Genotypes were selected from M1 (first generation) to M5 (fifth generation) based on saline and/or nonsaline soil productions. This research aims to evaluate the growth and production of sixth-generation (M6) and seven-generation (M7) black soybean mutant genotypes. The research was conducted in Karangharjo Village, Pulokulon Sub-district, Grobogan District, Central Java Province, Indonesia. The plant material was three genotypes of M6 black soybean mutants (BSMG VQ 05-256/1-6-2-28, BSMG VQ 05-400/1-2-2-6 and BSMG VQ 05-256/1-2-9-29), four genotypes of M7 black soybean mutants (BSMG VQ 06-256/1-6-2-28, BSMG VQ 06-400/1-2-2-6 and BSMG VQ 06-256/1-2-9-29 and BSMG VQ 06-256/1-4-2-21) and three cultivar checks (Detam 1, Detam 3/parent variety and Detam 4 variety). The parameters measured consist of plant growth, components, and production. All data collected were subjected to statistical Analysis of Variance (ANOVA); if significantly different, it continued by Duncan Multiple Range Test (DMRT). The results showed that the genotype treatment affected all observed characters except plant height. Selected lines based on the number of leaves, number of pods, number of seeds, weight of 100 seeds, weight of seed, and production were BSMG VQ 05-256/1-2-9-29, BSMG VQ 05-256/1-2-9-29 and BSMG VQ 06-256/1-4-2-21. These selected genotypes provided the prospective source of soy sauce material and needed to examine its stability at different locations (multilocation test).

Bio-efficacy of mustard seed extracts against Bihar hairy caterpillar Spilosoma obliqua (Erebidae: Lepidoptera) & assessment of mustard allelo-chemicals in response to mustard aphid Lipaphis erysimi (Aphididae: Hemiptera) infestation

Mustard seed contains glucosinolate-myrosinase system of substrate-enzyme metabolism, accompanied with compartmentalized cells. Upon rupture, enzyme myrosinase leads to breakdown of glucosinolates and its metabolized products like allyl, benzyl, phenyl type of isothiocyantes and many other types like nitriles are released. The myrosinase activity is tested in three globally utilized different seed coat color mustards viz., brown mustard (Brassica juncea), white mustard (Sinapis alba) and black mustard (Brassica nigra) to demonstrate the release of glucosinolates which are known to deter insect pests. Aqueous seed extracts of these mustard types were subjected to anti-feedant activity analysis and oil extracted from these mustard seeds was subjected to insecticidal activity analysis against Spilosoma obliqua 4th instars on castor leaves. Meanwhile, the mustard leaves in open field were allowed for natural aphid infestation during early months from January to March. Thereafter, the leaf twigs of white, black and brown mustard, infested and uninfested by aphids, were collected and myrosinase activity of plants was analyzed with varying levels of important pest inflicted biochemicals in plant, viz., Total phenols, ortho-dihydric phenols and flavonols. Gas Chromatography–Mass Spectrometry analysis of mustard oil used in insecticidal activity was performed to elucidate the role of biochemicals involved in action. These compounds along with fatty acids and sterols compounds are known to have anti-feedant & insecticidal activities. Aqueous extract components were also subjected to total glucosinolate analysis, spectrophotometrically for knowing their concentration, with highest in brown (85.81 µmol/g) followed by black (59.32 µmol/g) and lowest in white mustard (47.63 µmol/g). The amount of glucosinolates, free fatty acids & sterol compounds present in different coat color mustard seed types are being correlated here with their potential bioactivities against biological plant pests. Bio-control of potentially harmful insect pests is possible by utilizing anti-feeding & insecticidal potential of mustard seed extracts.

Creating yellow seed Camelina sativa with enhanced oil accumulation by CRISPR‐mediated disruption of Transparent Testa 8

SummaryCamelina (Camelina sativa L.), a hexaploid member of the Brassicaceae family, is an emerging oilseed crop being developed to meet the increasing demand for plant oils as biofuel feedstocks. In other Brassicas, high oil content can be associated with a yellow seed phenotype, which is unknown for camelina. We sought to create yellow seed camelina using CRISPR/Cas9 technology to disrupt its Transparent Testa 8 (TT8) transcription factor genes and to evaluate the resulting seed phenotype. We identified three TT8 genes, one in each of the three camelina subgenomes, and obtained independent CsTT8 lines containing frameshift edits. Disruption of TT8 caused seed coat colour to change from brown to yellow reflecting their reduced flavonoid accumulation of up to 44%, and the loss of a well‐organized seed coat mucilage layer. Transcriptomic analysis of CsTT8‐edited seeds revealed significantly increased expression of the lipid‐related transcription factors LEC1, LEC2, FUS3, and WRI1 and their downstream fatty acid synthesis‐related targets. These changes caused metabolic remodelling with increased fatty acid synthesis rates and corresponding increases in total fatty acid (TFA) accumulation from 32.4% to as high as 38.0% of seed weight, and TAG yield by more than 21% without significant changes in starch or protein levels compared to parental line. These data highlight the effectiveness of CRISPR in creating novel enhanced‐oil germplasm in camelina. The resulting lines may directly contribute to future net‐zero carbon energy production or be combined with other traits to produce desired lipid‐derived bioproducts at high yields.

SUnSeT: spectral unmixing of hyperspectral images for phenotyping soybean seed traits

Key messageHyperspectral features enable accurate classification of soybean seeds using linear discriminant analysis and GWAS for novel seed trait genes.Evaluating crop seed traits such as size, shape, and color is crucial for assessing seed quality and improving agricultural productivity. The introduction of the SUnSet toolbox, which employs hyperspectral sensor-derived image analysis, addresses this necessity. In a validation test involving 420 seed accessions from the Korean Soybean Core Collections, the pixel purity index algorithm identified seed- specific hyperspectral endmembers to facilitate segmentation. Various metrics extracted from ventral and lateral side images facilitated the categorization of seeds into three size groups and four shape groups. Additionally, quantitative RGB triplets representing seven seed coat colors, averaged reflectance spectra, and pigment indices were acquired. Machine learning models, trained on a dataset comprising 420 accession seeds and 199 predictors encompassing seed size, shape, and reflectance spectra, achieved accuracy rates of 95.8% for linear discriminant analysis model. Furthermore, a genome-wide association study utilizing hyperspectral features uncovered associations between seed traits and genes governing seed pigmentation and shapes. This comprehensive approach underscores the effectiveness of SUnSet in advancing precision agriculture through meticulous seed trait analysis.

Natural variation in tocopherols, B vitamins, and isoflavones in seeds of 13 Korean conventional soybean varieties

Soybean seeds are excellent sources of tocopherols, B vitamins, and isoflavones, which are well known for their health benefits. This study investigated the influence of environment and genotype on these constituents across 13 Korean soybean varieties cultivated in three locations during the 2017–2019 growing seasons. Statistical analyses, employing both univariate and multivariate methods, revealed significant impacts of genetic and environmental factors on the composition of tocopherols, B vitamins, and isoflavones. Through permutational univariate analysis of variance, the primary contributors to each measured component were identified. Genotype strongly influenced the levels of β- and δ-tocopherols, whereas the interaction between location and year predominantly affected α- and γ-tocopherols. Vitamin B1 content was predominantly determined by genotype, whereas B3 and B6 were influenced by annual variations. Vitamin B2 level was primarily affected by the interplay between environmental and genotypic effects. Genotype had a significant effect on isoflavone components, with the exception of daidzein. Furthermore, early maturing varieties and those with black seed coats exhibited low levels of isoflavone components and total isoflavones, suggesting a relationship between maturity group and seed coat color in isoflavone variation. These findings can be used as reference values for compositional equivalence assessment of genetically modified soybeans.

Seed-Coat Pigmentation Plays a Crucial Role in Partner Selection and N2 Fixation in Legume-Root-Microbe Associations in African Soils.

Legume-rhizobia symbiosis is the most important plant-microbe interaction in sustainable agriculture due to its ability to provide much needed N in cropping systems. This interaction is mediated by the mutual recognition of signaling molecules from the two partners, namely legumes and rhizobia. In legumes, these molecules are in the form of flavonoids and anthocyanins, which are responsible for the pigmentation of plant organs, such as seeds, flowers, fruits, and even leaves. Seed-coat pigmentation in legumes is a dominant factor influencing gene expression relating to N2 fixation and may be responsible for the different N2-fixing abilities observed among legume genotypes under field conditions in African soils. Common bean, cowpea, Kersting's groundnut, and Bambara groundnut landraces with black seed-coat color are reported to release higher concentrations of nod-gene-inducing flavonoids and anthocyanins compared with the Red and Cream landraces. Black seed-coat pigmentation is considered a biomarker for enhanced nodulation and N2 fixation in legumes. Cowpea, Bambara groundnut, and Kersting's bean with differing seed-coat colors are known to attract different soil rhizobia based on PCR-RFLP analysis of bacterial DNA. Even when seeds of the same legume with diverse seed-coat colors were planted together in one hole, the nodulating bradyrhizobia clustered differently in the PCR-RFLP dendrogram. Kersting's groundnut, Bambara groundnut, and cowpea with differing seed-coat colors were selectively nodulated by different bradyrhizobial species. The 16S rRNA amplicon sequencing also found significant selective influences of seed-coat pigmentation on microbial community structure in the rhizosphere of five Kersting's groundnut landraces. Seed-coat color therefore plays a dominant role in the selection of the bacterial partner in the legume-rhizobia symbiosis.

Assessment of genotypic variability and genome‐wide association analysis of cooking time and canning quality traits in common bean (Phaseolus vulgaris L.)

AbstractDeveloping improved common bean varieties with short cooking time (CT) and good canning quality traits (CQTs) is very key for accelerating bean consumption among the urban and middle‐class population. The objective of this study was to assess the genotypic variability and identify single nucleotide polymorphism (SNP) markers associated with CT and CQTs in common bean. A total of 250 common bean accessions were evaluated under field conditions for two seasons using alpha lattice design with two replications. Three months post‐harvest, the dry bean grains were evaluated for CT and CQTs. Significant variation was observed among the 250 common bean accessions tested for both traits. CT ranged from 51 to 215 min, with 11 genotypes cooking in less than 60 min. The percentage total CQTs' score ranged from 41% to 84% with 31 genotypes scoring 76% and above. Forty‐seven significant GWAS signals were detected for CT on chromosomes Pv01, Pv04, Pv05 and Pv11 and CQTs on Pv01, Pv02, Pv03, Pv04, Pv05, Pv06, Pv07, Pv08, Pv10 and Pv11, respectively. Positional candidate genes including Phvul.005G161200 on chromosome Pv05, Phvul.007G2803001 and Phvul.007G280700 on chromosome Pv07 were associated with seed coat colour retention of the canned beans. Besides their usefulness in breeding research, the identified bean genotypes with shorter CT and good CQTs could enhance bean consumption and processing industries.

Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L.

The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs AX-95172164 (chromosome 1B) and AX-158544327 (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was TraesCS6B02G147900, encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known Tamyb10 gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified TraesCS1D03G0758600 and TraesCS7B03G1296800, involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.

Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach.

This study investigates the genetic determinants of seed coat color and pattern variations in cowpea (Vigna unguiculata), employing a genome-wide association approach. Analyzing a mapping panel of 296 cowpea varieties with 110,000 single nucleotide polymorphisms (SNPs), we focused on eight unique coat patterns: (1) Red and (2) Cream seed; (3) White and (4) Brown/Tan seed coat; (5) Pink, (6) Black, (7) Browneye and (8) Red/Brown Holstein. Across six GWAS models (GLM, SRM, MLM, MLMM, FarmCPU from GAPIT3, and TASSEL5), 13 significant SNP markers were identified and led to the discovery of 23 candidate genes. Among these, four specific genes may play a direct role in determining seed coat pigment. These findings lay a foundational basis for future breeding programs aimed at creating cowpea varieties aligned with consumer preferences and market requirements.

Omics-driven advances in the understanding of regulatory landscape of peanut seed development.

Peanuts (Arachis hypogaea) are an essential oilseed crop known for their unique developmental process, characterized by aerial flowering followed by subterranean fruit development. This crop is polyploid, consisting of A and B subgenomes, which complicates its genetic analysis. The advent and progression of omics technologies-encompassing genomics, transcriptomics, proteomics, epigenomics, and metabolomics-have significantly advanced our understanding of peanut biology, particularly in the context of seed development and the regulation of seed-associated traits. Following the completion of the peanut reference genome, research has utilized omics data to elucidate the quantitative trait loci (QTL) associated with seed weight, oil content, protein content, fatty acid composition, sucrose content, and seed coat color as well as the regulatory mechanisms governing seed development. This review aims to summarize the advancements in peanut seed development regulation and trait analysis based on reference genome-guided omics studies. It provides an overview of the significant progress made in understanding the molecular basis of peanut seed development, offering insights into the complex genetic and epigenetic mechanisms that influence key agronomic traits. These studies highlight the significance of omics data in profoundly elucidating the regulatory mechanisms of peanut seed development. Furthermore, they lay a foundational basis for future research on trait-related functional genes, highlighting the pivotal role of comprehensive genomic analysis in advancing our understanding of plant biology.