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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Seed coat color affects the appearance and commodity quality of mung beans (Vigna radiata L.). The substances that affect mung bean seed coat color are mainly flavonoids, which have important medicinal value. Mapping the seed coat color gene in mung beans would facilitate the development of new varieties and improve their value. In this study, an F2 mapping population consisting of 546 plants was constructed using Jilv9 (black seed coat) and BIS9805 (green seed coat). Using bulk segregated analysis (BSA) sequencing and kompetitive allele-specific PCR (KASP) markers, the candidate region related to seed coat color was finally narrowed to 0.66 Mb on chromosome (Chr.) 4 and included eight candidate genes. Combined transcriptome and metabolome analyses showed that three of the eight candidate genes (LOC106758748, LOC106758747, and LOC106759075) were differentially expressed, which may have caused the differences in flavonoid metabolite content between Jilv9 and BIS9805. These findings can provide a research basis for cloning the genes related to seed coat color and accelerate molecular marker-assisted selection breeding in mung beans.

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. [ABSTRACT FROM AUTHOR]

Sesame seeds are important resources for relieving oxidation stress-related diseases. Although a significant variation in seeds' antioxidant capability is observed, the underlying biochemical and molecular basis remains elusive. Thus, this study aimed to reveal major seed components and key molecular mechanisms that drive the variability of seeds' antioxidant activity (AOA) using a panel of 400 sesame accessions. The seeds' AOA, total flavonoid, and phenolic contents varied from 2.03 to 78.5%, 0.072 to 3.104 mg CAE/g, and 2.717 to 21.98 mg GAE/g, respectively. Analyses revealed that flavonoids and phenolic acids are the main contributors to seeds' AOA variation, irrespective of seed coat color. LC-MS-based polyphenol profiling of high (HA) and low (LA) antioxidant seeds uncovered 320 differentially accumulated phenolic compounds (DAPs), including 311 up-regulated in HA seeds. Tricin, persicoside, 5,7,4′,5′-tetrahydro-3′,6-dimethoxyflavone, 8-methoxyapigenin, and 6,7,8-tetrahydroxy-5-methoxyflavone were the top five up-regulated in HA. Comparative transcriptome analysis at three seed developmental stages identified 627~2357 DEGs and unveiled that differential regulation of flavonoid biosynthesis, phenylpropanoid biosynthesis, and stilbene biosynthesis were the key underlying mechanisms of seed antioxidant capacity variation. Major differentially regulated phenylpropanoid structural genes and transcription factors were identified. SINPZ0000571 (MYB), SINPZ0401118 (NAC), and SINPZ0500871 (C3H) were the most highly induced TFs in HA. Our findings may enhance quality breeding. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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Seed coat color is an important consumer-related trait of the cowpea (Vigna unguiculata [L.] Walp.) and has been a subject of study for over a century. Utilizing newly available resources, including mapping populations, a high-density genotyping platform, and several genome assemblies, the red seed coat color has been mapped to two loci, Red-1 (R-1) and Red-2 (R-2), on Vu03 and Vu07, respectively. A gene model (Vigun03g118700) encoding a dihydroflavonol 4-reductase, a homolog of anthocyanidin reductase 1, which catalyzes the biosynthesis of epicatechin from cyanidin, has been identified as a candidate gene for R-1. Possible causative variants have also been identified for Vigun03g118700. A gene model on Vu07 (Vigun07g118500), with predicted nucleolar function and high relative expression in the developing seed, has been identified as a candidate for R-2. The observed red color is believed to be the result of a buildup of cyanidins in the seed coat. [ABSTRACT FROM AUTHOR]

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.

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.

Perilla seeds are essential functional foods and key ingredients in traditional medicine. Herein, we investigated the variation in phytochemical profiles and antioxidant activities of twelve different perilla seeds. The seeds showed significant variations in total phenolic and flavonoid contents ranging from 16.92 to 37.23 mg GAE/g (GAE, gallic acid equivalent) and 11.6 to 19.52 mg CAE/g (CAE, catechin equivalent), respectively. LC-QqQ-MS (liquid chromatography triple quadrupole tandem mass spectrometry)-based widely targeted metabolic profiling identified a total of 975 metabolites, including 68–269 differentially accumulated metabolites (DAMs). Multivariate analyses categorized the seeds into four groups based on the seed coat and leaf colors. Most key bioactive DAMs, including flavonoids (quercetin-3'-O-glucoside, prunin, naringenin, naringenin chalcone, butin, genistin, kaempferol-3-O-rutinoside, etc.), amino acids (valine, lysine, histidine, glutamine, threonine, etc.), and vitamins (B1, B3, B6, U, etc.) exhibited the highest relative content in PL3 (brown seed, purple leaf), PL1 (white seed, green-purple leaf), and PL4 (white seed, green leaf) groups, respectively. Meanwhile, key differentially accumulated phenolic acids showed a higher relative content in PL1 and PL4 than in other groups. Both seeds exhibited high antioxidant activities, although those of PL2 (brown seed, green leaf) group seeds were the lowest. Our results may facilitate the comprehensive use of perilla seeds in food and pharmaceutical industries. [ABSTRACT FROM AUTHOR]

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.

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.

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.

Sesame seeds are important resources for relieving oxidation stress-related diseases. Although a significant variation in seeds’ antioxidant capability is observed, the underlying biochemical and molecular basis remains elusive. Thus, this study aimed to reveal major seed components and key molecular mechanisms that drive the variability of seeds’ antioxidant activity (AOA) using a panel of 400 sesame accessions. The seeds’ AOA, total flavonoid, and phenolic contents varied from 2.03 to 78.5%, 0.072 to 3.104 mg CAE/g, and 2.717 to 21.98 mg GAE/g, respectively. Analyses revealed that flavonoids and phenolic acids are the main contributors to seeds’ AOA variation, irrespective of seed coat color. LC-MS-based polyphenol profiling of high (HA) and low (LA) antioxidant seeds uncovered 320 differentially accumulated phenolic compounds (DAPs), including 311 up-regulated in HA seeds. Tricin, persicoside, 5,7,4′,5′-tetrahydro-3′,6-dimethoxyflavone, 8-methoxyapigenin, and 6,7,8-tetrahydroxy-5-methoxyflavone were the top five up-regulated in HA. Comparative transcriptome analysis at three seed developmental stages identified 627~2357 DEGs and unveiled that differential regulation of flavonoid biosynthesis, phenylpropanoid biosynthesis, and stilbene biosynthesis were the key underlying mechanisms of seed antioxidant capacity variation. Major differentially regulated phenylpropanoid structural genes and transcription factors were identified. SINPZ0000571 (MYB), SINPZ0401118 (NAC), and SINPZ0500871 (C3H) were the most highly induced TFs in HA. Our findings may enhance quality breeding.

GAMMA irradiation might be an alternative strategy for increasing crop yield and/or introducing new varieties. Reddish-brown Phaseolus vulgaris L. cv Abo Yousuf was exposed to 50Gy of γ-radiation produced M2 seeds, while 100 and 300Gy were lethal. M2 seeds were cultivated to investigate the segregated traits in M3 and M4 plants. Segregation of purple and green: hypocotyls, lower venation, and pods, besides purple flowers and emarginated leaf apex, were observed in M3 plants. M3 seeds showed five seed coat colors: reddish-brown, brown, dark brown, grayish brown, and gray. The reddish-brown seeds had the highest weight, 30.74%, whereas the gray seeds had a much lighter weight, 23.14%. The flower color was light purple in three lines viz; control, M2 50Gy, and M3 reddish brown and white in M3 dark brown line. While M3 brown and gray seeds produced four flower colors: dark purple, purple, light purple, and white. Whereas, M3 grayish brown seeds produced three flower colors: dark purple, purple, and white. Furthermore, γ-radiation induced 15 new seed coat colors in M4 progeny. Molecular characterization showed different fingerprints correlated with the segregated morphological traits and seed coat colors. Both the PCR fingerprints and the dendrograms produced by cluster analysis of the selected four RAPD differentiated clearly between the different M3 segregating genotypes of cv Abo Yousuf from M2 and control plants more than the two ISSR primers. Such findings indicated the pleiotropic effects of seed coat color genes and provided helpful information on gene(s) that govern these traits. [ABSTRACT FROM AUTHOR]

In urban forestry plantations are implemented in different cities of the world for social and environmental benefits. Bauhinia retusa and Bauhinia variegata are important species and to be used as large-scale plantation programs in urban forestry which might solve or mitigate urban, social, and environmental issues such as improving the physical & mental health of residents, food and nutrition security, increasing urban biodiversity, cooling the neighboring, preventing soil erosion, flooding, and mitigating greenhouse gas emissions and air pollution. The present study was conducted with the aim of producing quality planting material for B. retusa and B. variegata in the nursery for afforestation programs. Seeds of B. retusa and B. variegata were collected from the natural habitats to assess seed germination and seedling growth. Seeds were stored in different types of containers at room temperature and later on exposed to 15, 20, and 25 °C in seed germinator. Seeds were further sown in polythene bags according to the seed size, seed coat color, seed sowing depth, the orientation of seeds, and the result of the emergence of seedlings, their growth, and biomass were estimated. A two-way analysis of variance was calculated to estimate the variation among the studied parameters. Results revealed that a constant 25 °C temperature was considered best for seed germination of both the Bauhinia species. Polybags were found the most suitable for storing the Bauhinia seeds among the storage containers. The seedling emergence and growth were maximum in yellow color and large seeds. In B. retusa, seedling emergence, and growths were the maximum in seeds sown at a horizontal position and in B. variegata at an upright position. Seedling emergence, length, and biomass were recorded the maximum when seeds of B. retusa were sown at 4 cm depth and B. variegata seeds were sown at 2 cm depth. The study recommends that the yellow color seed that has to be sown at 2 cm to 4 cm depth with upright and horizontal positions is considered best for the production of quality planting stock of both studied Bauhinia species. [ABSTRACT FROM AUTHOR]

Abstract Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B. napus (AACC) and the worst in B. carinata (BBCC). The comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.

Seed coat color is an important consumer-related trait of the cowpea (Vigna unguiculata [L.] Walp.) and has been a subject of study for over a century. Utilizing newly available resources, including mapping populations, a high-density genotyping platform, and several genome assemblies, the red seed coat color has been mapped to two loci, Red-1 (R-1) and Red-2 (R-2), on Vu03 and Vu07, respectively. A gene model (Vigun03g118700) encoding a dihydroflavonol 4-reductase, a homolog of anthocyanidin reductase 1, which catalyzes the biosynthesis of epicatechin from cyanidin, has been identified as a candidate gene for R-1. Possible causative variants have also been identified for Vigun03g118700. A gene model on Vu07 (Vigun07g118500), with predicted nucleolar function and high relative expression in the developing seed, has been identified as a candidate for R-2. The observed red color is believed to be the result of a buildup of cyanidins in the seed coat.

Brassica juncea L. is an important oilseed crop that yields edible oil and biofuel. Improving B. juncea seed traits is a primary breeding target, but these traits are genetically complex. MicroRNAs (miRNAs) regulate seed development by modulating gene expression at the post-transcriptional or translational level and are excellent candidates for improving seed traits. However, the roles of miRNAs in B. juncea seed development are yet to be investigated. Here, we report small RNA profiling and miRNA identification from developing seeds of two contrasting varieties of B. juncea, Early Heera2 (EH2) and Pusa Jaikisan (PJK). We identified 326 miRNAs, including 127 known and 199 novel miRNAs, of which 103 exhibited inter-varietal differential expression. Integrating miRNAome and our previous transcriptome data identified 13,683 putative miRNA-target modules. Segregation of differentially expressed miRNAs into different groups based on variety-wise upregulation, followed by comprehensive functional analysis of targets using pathway mapping, gene ontology, transcription factor mapping, and candidate gene analysis, revealed at least 11, 6, and 7 miRNAs as robust candidates for the regulation of seed size, seed coat color, and oil content, respectively. Further, co-localization with previously reported quantitative trait loci (QTL) proffered 29 and 15 miRNAs overlapping with seed weight and oil content QTLs, respectively. Our study is the first comprehensive report of miRNAome expression dynamics from developing seeds and provides candidate miRNAs and target genes for engineering seed traits in B. juncea.

Seed coat color is a typical morphological trait that can be used to reveal the evolution of soybean. The study of seed coat color-related traits in soybeans is of great significance for both evolutionary theory and breeding practices. In this study, 180 F10 recombinant inbred lines (RILs) derived from the cross between the yellow-seed coat cultivar Jidou12 (ZDD23040, JD12) and the wild black-seed coat accession Y9 (ZYD02739) were used as materials. Three methods, single-marker analysis (SMA), interval mapping (IM), and inclusive composite interval mapping (ICIM), were used to identify quantitative trait loci (QTLs) controlling seed coat color and seed hilum color. Simultaneously, two genome-wide association study (GWAS)models, the generalized linearmodel (GLM) and mixed linearmodel (MLM), were used to jointly identify seed coat color and seed hilum color QTLs in 250 natural populations. By integrating the results from QTL mapping and GWAS analysis, we identified two stable QTLs (qSCC02 and qSCC08) associated with seed coat color and one stable QTL (qSHC08) related to seed hilum color. By combining the results of linkage analysis and association analysis, two stable QTLs (qSCC02, qSCC08) for seed coat color and one stable QTL (qSHC08) for seed hilum color were identified. Upon further investigation using Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we validated the previous findings that two candidate genes (CHS3C and CHS4A) reside within the qSCC08 region and identified a new QTL, qSCC02. There were a total of 28 candidate genes in the interval, among which Glyma.02G024600, Glyma.02G024700, and Glyma.02G024800 were mapped to the glutathione metabolic pathway, which is related to the transport or accumulation of anthocyanin. We considered the three genes as potential candidate genes for soybean seed coat-related traits. The QTLs and candidate genes detected in this study provide a foundation for further understanding the genetic mechanisms underlying soybean seed coat color and seed hilum color and are of significant value in marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Brassica juncea has adapted to diverse climate zones and latitudes, especially in the Yunnan-Guizhou Plateau with the complexity and diversity of the ecological types of western China. However, the genetic variations underlying the diversity of these ecotypes are poorly known. In this study, we resequenced the genome of 193 indigenous B. juncea accessions and obtained 1.04 million high-quality SNPs and 3.23 million InDels by mapping reads to the reference genomes of B. juncea var. timuda. Phenotype, population genetic, phylogenetic and principal component analyses showed considerable genetic variation including four distinct genetic groups. Selective sweep analysis and a genome-wide association study revealed the candidate genes for seed color and fatty acid biosynthesis. The results provide a comprehensive insight into the spread and improvement of B. juncea and laya foundation for accelerating rapeseed breeding by facilitating screenings of molecular markers. [ABSTRACT FROM AUTHOR]

Safflower is an important oilseed crop cultivated primarily for its seeds, which have pharmaceutical properties. Color is an important agronomical trait that appears to be a prior parameter for evaluating the internal quality of plant seeds. This study employs 197 safflower accessions seeds to analyze how their seed coat and flower colors affect their total oil content, fatty acid composition, total phenolic content (TPC), N-(p-coumaroyl)serotonin (CS) and N-feruloylserotonin (FS) contents, and [2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)] radical scavenging activities. Significant variations were observed in the targeted metabolite contents and antioxidant properties among genotypes. Notably, the linoleic acid content, total unsaturated fatty acid content, the ratio of total unsaturated fatty acid to total saturated fatty acid, CS, FS, ABTS, and DPPH scavenging capacities varied significantly based on seed coat color, with white-seeded genotypes having the highest average values of these parameters. Moreover, the linoleic acid content differed significantly (p < 0.05) among the genotypes with varying flower colors, with white-flowered accessions having the highest average content. Furthermore, genotypes K185105 (No. 75) and K175278 (No. 146) were identified as promising genetic resources with health benefits. Overall, these findings reveal that seed coat and flower colors distinctly affect metabolite contents and antioxidant properties in safflower seeds. [ABSTRACT FROM AUTHOR]

Abstract Seed coat color is an important quality and domestication trait. The adzuki bean has more than a dozen seed coat colors closely associated with the anthocyanin and flavonoid metabolism pathways. In this study, we explored the pigment composition of 10 different seed coat color adzuki beans including red, black mottle on red, black mottle on gray, golden, green, black, ivory, brown, and light brown. The results showed that anthocyanins are the main pigment in adzuki bean seed coat. There were no carotenoid or pelargonidin derivatives in the seed coats of any accessions. Different colors of adzuki bean seed coat have different pigment compositions and the combination of procyanidins and anthocyanins affected seed coat color. The ivory seed coat had an extremely low proanthocyanidin and anthocyanin content. Only the green adzuki bean seed coats contained chlorophyll. Our results explain the pigment composition of the different seed coat colors and the combination of proanthocyanidins and anthocyanins affected seed coat color in adzuki bean. These results can provide a theoretical basis for the study of adzuki bean coloring mechanism.

Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B. napus (AACC) and the worst in B. carinata (BBCC). The comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids. [ABSTRACT FROM AUTHOR]

Brassica juncea is a major oilseed crop of Bangladesh, Canada, China, India, Pakistan, and the USA. The genome and pan-genome sequencing of B. juncea revealed that the gene pool maintained uniformity till now since its origin. Moreover, the selection process for higher yield and quality favors genetic homogeneity in the crop making it vulnerable to biotic and abiotic stresses. To resolve the existing problem, we have developed allohexaploid Brassica with S. alba and B. juncea by somatic hybridization. Backcross lines (BLs) from allohexaploid Brassica have been developed by backcrossing with B. juncea to transfer desirable genes for biotic and abiotic tolerance into the Brassica genome background. The first backcross population had few apparent phenotypic variations, while the second backcross generation exhibited enormous variations in agronomic characteristics and stem rot disease resistance. These BLs had plant heights, siliquae size, seeds/siliqua, seeds/plant, and 1000 seed weights of 147.6–249.6 cm, 2.88–6.5 cm, 4.4–19, 3.55–30.04 g, and 1.19–4.83 g, respectively. In terms of immunity to Sclerotinia stem rot (SSR), the BL 58 had the longest siliquae (6.5 cm) and the highest thousand seed weight (4.83 g). These BLs produced seeds that range in color from black to yellow, with varying hues of brown. The BLs were found immune to being highly susceptible to the SSR. These BLs outperform their parent in terms of agronomic traits like yellow/brown seed color, stem rot resistance, seeds/siliqua, and seed weight per plant, as well as excellent fertility. As a result, these BLs can be utilized to identify QTLs, marker assisted breeding, resistance breeding, and introgression of valuable traits to cultivated Brassica species. [ABSTRACT FROM AUTHOR]

Introduction: Sesameseedshavebecomeanirreplaceablesourceofedibleoilsand food products with rich nutrients and a unique flavor, and theirmetabolite contents and physiological functions vary widely across different seed coat colors. Although the quantitative trait loci (QTLs) for genetic variation in seed coat color have been extensively investigated, the identification of unique genetic loci for intermediate colors such as brown has not been reported due to their complexity. Methods: Here, we crossed the white sesame 'Yuzhi No. 8' (YZ8) and the brown sesame 'Yanzhou Erhongpi' (YZEHP) to construct a recombinant inbred line (RIL) population with consecutive self-fertilization for ten generations. Results: The selfed F1 seeds were brown which was controlled by a dominant gene. Based on the genotyping by whole-genome resequencing of the RILs, a major-effect QTL for brown coat color was identified through both bulk segregant analysis (BSA) and genetic linkage mapping in sesame, which was located within a 1.19 Mb interval on chromosome 6 (qBSCchr6). Moreover, we found that the YZEHP seed coat initially became pigmented at 20 days postanthesis (DPA) and was substantially colored at 30 DPA. We screened 13 possible candidate genes based on the effects of genetic variants on protein coding and predicted gene functions. Furthermore, qRT-PCR was used to verify the expression patterns of these genes in different post-anthesis developmental periods. We noted that in comparison to YZ8 seeds, YZEHP seeds had expression of SIN_1023239 that was significantly up-regulated 2.5-, 9.41-, 6.0-, and 5.9-fold at 15, 20, 25, and 30 DPA, respectively, which was consistent with the pattern of brown seed coat pigment accumulation. Discussion: This study identified the first major-effect QTL for the control of the brown seed coat trait in sesame. This finding lays the foundation for further fine mapping and cloning as well as investigating the regulatory mechanism of seed coat color in sesame [ABSTRACT FROM AUTHOR]

The DPPH radical scavenging activity and ORAC value of soybeans (yellow soybean, blue soybean, and black soybean) were increased by roasting at above 190 °C. Concerning raw beans, black soybeans with the darkest seed coat color had the strongest antioxidant activity, indicating the effect of the coat pigment. However, the degree of increased antioxidant activity by roasting was almost similar regardless of seed coat color, suggesting that coat color is independent of the increased antioxidant activity. Concerning aged beans stored at 37 °C/75% RH for 60 days, the antioxidant activity increased in yellow soybean and decreased in blue and black soybean compared to before storage. Conversely, when roasted at 190 °C for 20 min, the DPPH values of all the aged beans were significantly increased. Other analyses of roasted beans with and without seed coat showed that changes in the components of cotyledons during storage may have contributed to the increased antioxidant activity of aged beans, regardless of seed coat color. These results revealed that roasting effectively improves the antioxidant activity of aged soybeans, regardless of seed coat color. We concluded that roasting is recommended for antioxidant properties, particularly regarding the effective use of aged beans. [ABSTRACT FROM AUTHOR]

Perilla seeds are essential functional foods and key ingredients in traditional medicine. Herein, we investigated the variation in phytochemical profiles and antioxidant activities of twelve different perilla seeds. The seeds showed significant variations in total phenolic and flavonoid contents ranging from 16.92 to 37.23 mg GAE/g (GAE, gallic acid equivalent) and 11.6 to 19.52 mg CAE/g (CAE, catechin equivalent), respectively. LC-QqQ-MS (liquid chromatography triple quadrupole tandem mass spectrometry)-based widely targeted metabolic profiling identified a total of 975 metabolites, including 68–269 differentially accumulated metabolites (DAMs). Multivariate analyses categorized the seeds into four groups based on the seed coat and leaf colors. Most key bioactive DAMs, including flavonoids (quercetin-3’-O-glucoside, prunin, naringenin, naringenin chalcone, butin, genistin, kaempferol-3-O-rutinoside, etc.), amino acids (valine, lysine, histidine, glutamine, threonine, etc.), and vitamins (B1, B3, B6, U, etc.) exhibited the highest relative content in PL3 (brown seed, purple leaf), PL1 (white seed, green-purple leaf), and PL4 (white seed, green leaf) groups, respectively. Meanwhile, key differentially accumulated phenolic acids showed a higher relative content in PL1 and PL4 than in other groups. Both seeds exhibited high antioxidant activities, although those of PL2 (brown seed, green leaf) group seeds were the lowest. Our results may facilitate the comprehensive use of perilla seeds in food and pharmaceutical industries.

Seed coat color is an important part of consumer preferences for cowpea (Vigna unguiculata [L.] Walp). Color has been studied in numerous crop species and has often been linked to loci controlling the anthocyanin biosynthesis pathway. This study makes use of available resources, including mapping populations, a reference genome, and a high-density single nucleotide polymorphism genotyping platform, to map the black seed coat and purple pod tip color traits, with the gene symbol Bl, in cowpea. Several gene models encoding MYB domain protein 113 were identified as candidate genes. MYB domain proteins have been shown in other species to control expression of genes encoding enzymes for the final steps in the anthocyanin biosynthesis pathway. PCR analysis indicated that a presence/absence variation of one or more MYB113 genes may control the presence or absence of black pigment. A PCR marker has been developed for the MYB113 gene Vigun05g039500, a candidate gene for black seed coat color in cowpea.

Common bean (Phaseolus vulgaris L.) is the most widespread legume in Croatia and its production is based on landraces of great morphological diversity. Landraces morphologically differ the most in the seed coat color and size. Because plant emergence and crop establishment represent the most sensitive stage in crop development, the aim of this study was to determine whether the seed coat color and seed size of Croatian common bean landraces affect the water absorption rate, seed germination, emergence and phenotypic characteristics of the seedlings. In this study seeds of four common bean landraces with different seed color and size, 'Biser' (white-colored, small-seeded), 'Bijeli' (white-colored, large-seeded), 'Kornjača' (dark-colored, small-seeded) and 'Trešnjevac' (dark-colored, large-seeded) were evaluated in three different experiments: (i) water uptake, (ii) seed germination and (iii) emergence and seedling phenotypic characterization. The results show that white-colored seeds have a higher absorption rate and release more electrolytes compared to dark-colored seeds of similar size (and weight). The germination results show that white-colored and smaller seeds germinate faster compared to dark-colored and large seeds. On the other hand, the white-colored landrace 'Bijeli' took the longest time to emerge, probably due to cell damage that occurred during the fast initial water absorption. Using multispectral imaging, chlorophyll fluorescence imaging and stomatal conductance analysis, the seedlings of the dark-colored and large-seeded landraces were found to contain more photosynthetic pigments and have higher light absorption. In contrast, seedlings of white-colored and large seeds have lower stomatal conductance and transpiration and higher photochemical efficiency (despite possible cell damage during water absorption and germination). Results suggest that dark-colored seeds could survive better under unfavorable soil conditions without absorbing water, swelling, emergence or molding than white-colored seeds. Despite all this, white-colored common bean landraces remain popular in human diets and are often grown on small-scale farms. [ABSTRACT FROM AUTHOR]

The aim of this study was to analyze the physiological activity of 48 soybean resources harvested in 2020 to identify the soybean resources’ relationships with individual isoflavone compounds and their genetic properties. These data will subsequently be compared with the research results on soybeans harvested in 2019. Initially, with respect to the physiological activity (6 types) and substances (19 types), this study evaluated the differences between the cultivation year (two years), seed coat color (three colors), and the interaction of the year and seed coat color of soybeans through ANOVA. Among the physiological activities, there were differences in the estrogen, estrogen receptor alpha, and UCP-1 (uncoupling protein-1) activities depending on the cultivation year. Moreover, there were differences in NO (nitric oxide), revealing differences in the ABTS (2, 2′-azino-bis-3ethylbenzo-thiazoline-6-sulfonic acid) and DPPH (2, 2-diphenyl-2-picrylhydrazyl) radical scavenging activities due to the seed coat color and the interaction of the year and seed coat color. Soybeans harvested in 2020 exhibited increased ABTS, DPPH, and NO inhibitory activities and reduced estrogen, estrogen receptor alpha, and UCP-1 activities compared to those harvested in 2019. According to the ANOVA results, eight of the nineteen individual derivatives illustrated yearly differences, while three derivatives displayed differences due to the seed coat color. Secondly, according to the relationship between the efficacy, derivative substances, and genetic properties, it was determined that genistein 7-O-(2″-O-apiosyl)glucoside (F5) is the individual isoflavone derivative that affected the six types of physiological activity, on which the genome-wide association study (GWAS) showed no significant differences for genetic properties. These results were inconsistent with the 2019 data, where three types of individual compounds, including F5, were proposed as substances that correlated with efficacy and there was a high correlation with genetic properties. Therefore, this study selected B17, B23, B15, B24, and Y7 as excellent varieties that are stable and highly functional in the cultivation environment, producing only small annual differences. The results of this study will be utilized as basic data for predicting soybean varieties and their cultivation, which have high environmental stability under climate variation and properly retain the functional substances and efficacy. [ABSTRACT FROM AUTHOR]

Seed size and color are important traits of watermelon influencing consumer appeal and market acceptance. However, only few attempts have been made to dissect the genomic region or gene(s) determining these traits. The molecular regulatory mechanisms underlying these traits in watermelon are complex and still unclear. In the current experiment, we have made an attempt to map the QTLs for these seed traits in BC1F2 mapping population of cross BIL-53 (Citrullus amarus) × IIHR-140-152 (Citrullus lanatus). Analysis revealed two QTLs viz., q_100SW_2.1 and q_100SW_6.1 for 100seed weight; three QTLs viz., q_SCC_3.1, q_SCC_5.1 and q_SCC_5.2 for seed coat color. GO annotation of genes located in these QTL regions predicted putative candidate genes for seed size and color. The PCR based flanking markers identified in the current study for seed weight, BVWS02340 and BVWI00252 on chromosome 2, BVWS02424 and BVWS00117 on chromosome 6; for seed coat color, BVWS01383 on chromosome 3, BVWS01643 and BVWI00228, BWWS00854 and BVWS02096 on chromosome 5 can be used for marker assisted selection (MAS) of watermelon seed traits. [ABSTRACT FROM AUTHOR]

In urban forestry plantations are implemented in different cities of the world for social and environmental benefits. Bauhinia retusa and Bauhinia variegata are important species and to be used as large-scale plantation programs in urban forestry which might solve or mitigate urban, social, and environmental issues such as improving the physical & mental health of residents, food and nutrition security, increasing urban biodiversity, cooling the neighboring, preventing soil erosion, flooding, and mitigating greenhouse gas emissions and air pollution. The present study was conducted with the aim of producing quality planting material for B. retusa and B. variegata in the nursery for afforestation programs. Seeds of B. retusa and B. variegata were collected from the natural habitats to assess seed germination and seedling growth. Seeds were stored in different types of containers at room temperature and later on exposed to 15, 20, and 25 °C in seed germinator. Seeds were further sown in polythene bags according to the seed size, seed coat color, seed sowing depth, the orientation of seeds, and the result of the emergence of seedlings, their growth, and biomass were estimated. A two-way analysis of variance was calculated to estimate the variation among the studied parameters. Results revealed that a constant 25 °C temperature was considered best for seed germination of both the Bauhinia species. Polybags were found the most suitable for storing the Bauhinia seeds among the storage containers. The seedling emergence and growth were maximum in yellow color and large seeds. In B. retusa, seedling emergence, and growths were the maximum in seeds sown at a horizontal position and in B. variegata at an upright position. Seedling emergence, length, and biomass were recorded the maximum when seeds of B. retusa were sown at 4 cm depth and B. variegata seeds were sown at 2 cm depth. The study recommends that the yellow color seed that has to be sown at 2 cm to 4 cm depth with upright and horizontal positions is considered best for the production of quality planting stock of both studied Bauhinia species.

Abstract Background Pre-harvest sprouting (PHS) is a major problem for wheat production due to its direct detrimental effects on wheat yield, end-use quality and seed viability. Annually, PHS is estimated to cause > 1.0 billion USD in losses worldwide. Therefore, identifying PHS resistance quantitative trait loci (QTLs) is crucial to aid molecular breeding efforts to minimize losses. Thus, a doubled haploid mapping population derived from a cross between white-grained PHS susceptible cv AAC Innova and red-grained resistant cv AAC Tenacious was screened for PHS resistance in four environments and utilized for QTL mapping. Results Twenty-one PHS resistance QTLs, including seven major loci (on chromosomes 1A, 2B, 3A, 3B, 3D, and 7D), each explaining ≥10% phenotypic variation for PHS resistance, were identified. In every environment, at least one major QTL was identified. PHS resistance at most of these loci was contributed by AAC Tenacious except at two loci on chromosomes 3D and 7D where it was contributed by AAC Innova. Thirteen of the total twenty-one identified loci were located to chromosome positions where at least one QTL have been previously identified in other wheat genotype(s). The remaining eight QTLs are new which have been identified for the first time in this study. Pedigree analysis traced several known donors of PHS resistance in AAC Tenacious genealogy. Comparative analyses of the genetic intervals of identified QTLs with that of already identified and cloned PHS resistance gene intervals using IWGSC RefSeq v2.0 identified MFT-A1b (in QTL interval QPhs.lrdc-3A.1) and AGO802A (in QTL interval QPhs.lrdc-3A.2) on chromosome 3A, MFT-3B-1 (in QTL interval QPhs.lrdc-3B.1) on chromosome 3B, and AGO802D, HUB1, TaVp1-D1 (in QTL interval QPhs.lrdc-3D.1) and TaMyb10-D1 (in QTL interval QPhs.lrdc-3D.2) on chromosome 3D. These candidate genes are involved in embryo- and seed coat-imposed dormancy as well as in epigenetic control of dormancy. Conclusions Our results revealed the complex PHS resistance genetics of AAC Tenacious and AAC Innova. AAC Tenacious possesses a great reservoir of important PHS resistance QTLs/genes supposed to be derived from different resources. The tracing of pedigrees of AAC Tenacious and other sources complements the validation of QTL analysis results. Finally, comparing our results with previous PHS studies in wheat, we have confirmed the position of several major PHS resistance QTLs and candidate genes.

Tartary buckwheat, a polygonaceae family plant, is rich in abundant flavonoids, high-quality protein, and well-balanced essential amino acids. This study aimed to investigate the effects of climatic variables on the quality of Tartary buckwheat. In this study, six distinct types of Tartary buckwheat collected from the Sichuan Basin, Western Sichuan Plateau, and Yunnan-Guizhou Plateau in southwest China were chosen to investigate the impact of climatic conditions from the grain-filling stage to the harvest stage on the concentration of flavonoids and expression of key enzyme genes involved the synthesis of flavonoids. Meteorological data of three producing areas were collected from the China Meteorological Network, mainly including maximum temperature (Tmax), minimum temperature (Tmin), diurnal temperature difference (Tdif), and light intensity. Then, the contents of rutin, kaempferol-3-O-rutin glycoside, quercetin, and kaempferol in 30 batches of Tartary buckwheat from 6 varieties including Chuanqiao No. 1, Chuanqiao No. 2, Xiqiao No. 1, Xiqiao No. 2, Miqiao No. 1 and Di ku were determined by ultra performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Furthermore, the expression levels of phenylalanine ammonia lyase (PAL), 4-coumaric acid coenzyme A ligase (4CL), and anthocyanin synthase (ANS) in six kinds of Tartary buckwheat were detected by real-time polymerase chain reaction (PCR). The seed photos were processed by ImageJ processing software. The partial least squares method was used to analyze the correlation. As a result, light intensity can promote the accumulation of flavonoids and the expression of key enzyme genes. Miqiao No. 1, which grows in Liangshan Prefecture, Sichuan Province, has the highest light intensity and is the dominant variety with flavonoid content. More importantly, the expression levels of PAL and 4CL in the secondary metabolic pathway of flavonoids were positively correlated with the content of Tartary buckwheat flavonoids. Interestingly, the expression level of ANS was negatively correlated with the content of PAL, 4CL, and flavonoids. In addition, ANS is a key gene affecting the seed coat color of Tartary buckwheat. The higher the expression of ANS, the darker the seed coat color. These findings provide a theoretical basis and reference for the breeding of fine buckwheat varieties. [ABSTRACT FROM AUTHOR]

The size, shape, and color of wheat seeds are important traits that are associated with yield and flour quality (size, shape), nutritional value, and pre-harvest sprouting (coat color). These traits are under multigenic control, and to dissect their molecular and genetic basis, quantitative trait loci (QTL) analysis is used. We evaluated 114 recombinant inbred lines (RILs) in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative, ITMI/MP) grown in 2014 season. We used digital image analysis for seed phenotyping and obtained data for seven traits describing seed size and shape and 48 traits of seed coat color. We identified 212 additive and 34 pairs of epistatic QTLs on all the chromosomes of wheat genome except chromosomes 1A and 5D. Many QTLs were overlapping. We demonstrated that the overlap between QTL regions was low for seed size/shape traits and high for coat color traits. Using the literature and KEGG data, we identified sets of genes in Arabidopsis and rice from the networks controlling seed size and color. Further, we identified 29 and 14 candidate genes for seed size-related loci and for loci associated with seed coat color, respectively. [ABSTRACT FROM AUTHOR]

Seed coat color is an important quality and domestication trait. The adzuki bean has more than a dozen seed coat colors closely associated with the anthocyanin and flavonoid metabolism pathways. In this study, we explored the pigment composition of 10 different seed coat color adzuki beans including red, black mottle on red, black mottle on gray, golden, green, black, ivory, brown, and light brown. The results showed that anthocyanins are the main pigment in adzuki bean seed coat. There were no carotenoid or pelargonidin derivatives in the seed coats of any accessions. Different colors of adzuki bean seed coat have different pigment compositions and the combination of procyanidins and anthocyanins affected seed coat color. The ivory seed coat had an extremely low proanthocyanidin and anthocyanin content. Only the green adzuki bean seed coats contained chlorophyll. Our results explain the pigment composition of the different seed coat colors and the combination of proanthocyanidins and anthocyanins affected seed coat color in adzuki bean. These results can provide a theoretical basis for the study of adzuki bean coloring mechanism. [ABSTRACT FROM AUTHOR]

Seed coat color is a typical evolutionary trait. Identification of the genetic loci that control seed coat color during the domestication of wild soybean could clarify the genetic variations between cultivated and wild soybean. We used 276 F10 recombinant inbred lines (RILs) from the cross between a cultivated soybean (JY47) and a wild soybean (ZYD00321) as the materials to identify the quantitative trait loci (QTLs) for seed coat color. We constructed a high-density genetic map using re-sequencing technology. The average distance between adjacent markers was 0.31 cM on this map, comprising 9,083 bin markers. We identified two stable QTLs (qSC08 and qSC11) for seed coat color using this map, which, respectively, explained 21.933 and 26.934% of the phenotypic variation. Two candidate genes (CHS3C and CHS4A) in qSC08 were identified according to the parental re-sequencing data and gene function annotations. Five genes (LOC100786658, LOC100801691, LOC100806824, LOC100795475, and LOC100787559) were predicted in the novel QTL qSC11, which, according to gene function annotations, might control seed coat color. This result could facilitate the identification of beneficial genes from wild soybean and provide useful information to clarify the genetic variations for seed coat color in cultivated and wild soybean. [ABSTRACT FROM AUTHOR]

Brassica juncea has adapted to diverse climate zones and latitudes, especially in the Yunnan-Guizhou Plateau with the complexity and diversity of the ecological types of western China. However, the genetic variations underlying the diversity of these ecotypes are poorly known. In this study, we resequenced the genome of 193 indigenous B. juncea accessions and obtained 1.04 million high-quality SNPs and 3.23 million InDels by mapping reads to the reference genomes of B. juncea var. timuda. Phenotype, population genetic, phylogenetic and principal component analyses showed considerable genetic variation including four distinct genetic groups. Selective sweep analysis and a genome-wide association study revealed the candidate genes for seed color and fatty acid biosynthesis. The results provide a comprehensive insight into the spread and improvement of B. juncea and laya foundation for accelerating rapeseed breeding by facilitating screenings of molecular markers.

Seed coat color is one of the most intuitive phenotypes in bitter gourd (Momordica spp.). Although the inheritance of the seed coat color has been reported, the gene responsible for it is still unknown. This study used two sets of parents, representing, respectively, the intersubspecific and intraspecific materials of bitter gourd, and their respective F1 and F2 progenies for genetic analysis and primary mapping of the seed coat color. A large F2:3 population comprising 2,975 seedlings from intraspecific hybridization was used to fine-map the seed coat color gene. The results inferred that a single gene, named McSC1 , controlled the seed coat color and that the black color was dominant over the yellow color. The McSC1 locus was mapped to a region with a physical length of ∼7.8 Mb and 42.7 kb on pseudochromosome 3 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and linkage analysis, respectively. Subsequently, the McSC1 locus was further fine-mapped to a 13.2-kb region containing only one candidate gene, MC03g0810 , encoding a polyphenol oxidase (PPO). Additionally, the variations of MC03g0810 in the 89 bitter gourd germplasms showed a complete correlation with the seed coat color. Expression and PPO activity analyses showed a positive correlation between the expression level of MC03g0810 and its product PPO and the seed coat color. Therefore, MC03g0810 was proposed as the causal gene of McSC1. Our results provide an important reference for molecular marker-assisted breeding based on the seed coat color and uncover molecular mechanisms of the seed coat color formation in bitter gourd. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max (L.) Merrill) seeds are abundant in physiologically active metabolites, including carotenoids and chlorophylls, and are used as an affordable source of functional foods that promote and maintain human health. The distribution and variation of soybean seed metabolites are influenced by plant genetic characteristics and environmental factors. Here, we investigated the effects of germplasm origin, genotype, seed coat color and maturity group (MG) on the concentration variation of carotenoid and chlorophyll components in 408 soybean germplasm accessions collected from China, Japan, the USA and Russia. The results showed that genotype, germplasm origin, seed color, and MG were significant variation sources of carotenoid and chlorophyll contents in soybean seeds. The total carotenoids showed about a 25-fold variation among the soybean germplasms, with an overall mean of 12.04 µg g−1. Russian soybeans yielded 1.3-fold higher total carotenoids compared with Chinese and Japanese soybeans. Similarly, the total chlorophylls were substantially increased in Russian soybeans compared to the others. Soybeans with black seed coat color contained abundant concentrations of carotenoids, with mainly lutein (19.98 µg g−1), β-carotene (0.64 µg g−1) and total carotenoids (21.04 µg g−1). Concentrations of lutein, total carotenoids and chlorophylls generally decreased in late MG soybeans. Overall, our results demonstrate that soybean is an excellent dietary source of carotenoids, which strongly depend on genetic factors, germplasm origin, MG and seed coat color. Thus, this study suggests that soybean breeders should consider these factors along with environmental factors in developing carotenoid-rich cultivars and related functional food resources. [ABSTRACT FROM AUTHOR]

Seed coat color is one of the most intuitive phenotypes in bitter gourd (Momordica spp.). Although the inheritance of the seed coat color has been reported, the gene responsible for it is still unknown. This study used two sets of parents, representing, respectively, the intersubspecific and intraspecific materials of bitter gourd, and their respective F1 and F2 progenies for genetic analysis and primary mapping of the seed coat color. A large F2:3 population comprising 2,975 seedlings from intraspecific hybridization was used to fine-map the seed coat color gene. The results inferred that a single gene, named McSC1, controlled the seed coat color and that the black color was dominant over the yellow color. The McSC1 locus was mapped to a region with a physical length of ∼7.8 Mb and 42.7 kb on pseudochromosome 3 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and linkage analysis, respectively. Subsequently, the McSC1 locus was further fine-mapped to a 13.2-kb region containing only one candidate gene, MC03g0810, encoding a polyphenol oxidase (PPO). Additionally, the variations of MC03g0810 in the 89 bitter gourd germplasms showed a complete correlation with the seed coat color. Expression and PPO activity analyses showed a positive correlation between the expression level of MC03g0810 and its product PPO and the seed coat color. Therefore, MC03g0810 was proposed as the causal gene of McSC1. Our results provide an important reference for molecular marker-assisted breeding based on the seed coat color and uncover molecular mechanisms of the seed coat color formation in bitter gourd.

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Sesame is a worldwide oilseed crop used in the food pharmacy. Its seed phenotypes determine the seed quality values. However, a thorough assessment of seed coat metabolites is lacking, and the dark pigment in the seed coat is not well-characterized. Herein, we report the isolation of melanin by the alkali method from the black and brown sesame seeds. Physicochemical methods, including scanning electron microscopy (SEM), solubility, precipitation, UV-Vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, and thermogravimetric-differential scanning calorimetry (TG-DSC), were used to characterize the sesame melanins. The results clearly showed that the isolated pigments were similar to melanin from other sources. Both melanins were heat-stable and exhibited numerous characteristic absorption peaks. Through a comprehensible LC-MS/MS-based metabolome profiles analysis of NaOH and methanol extracts of black and white sesame seeds, caffeic, protocatechuic, indole-carboxylic, homogentisic, ferulic, vanillic, and benzoic acids were identified as the potential precursors of the sesame melanin. Our findings widen our understanding of dark seeds pigmentation in sesame. Furthermore, they show that black sesame seeds are promising sources of edible melanin for food and biotechnological applications.

Background: Pre-harvest sprouting (PHS) is a major problem for wheat production due to its direct detrimental effects on wheat yield, end-use quality and seed viability. Annually, PHS is estimated to cause > 1.0 billion USD in losses worldwide. Therefore, identifying PHS resistance quantitative trait loci (QTLs) is crucial to aid molecular breeding efforts to minimize losses. Thus, a doubled haploid mapping population derived from a cross between white-grained PHS susceptible cv AAC Innova and red-grained resistant cv AAC Tenacious was screened for PHS resistance in four environments and utilized for QTL mapping. Results: Twenty-one PHS resistance QTLs, including seven major loci (on chromosomes 1A, 2B, 3A, 3B, 3D, and 7D), each explaining ≥10% phenotypic variation for PHS resistance, were identified. In every environment, at least one major QTL was identified. PHS resistance at most of these loci was contributed by AAC Tenacious except at two loci on chromosomes 3D and 7D where it was contributed by AAC Innova. Thirteen of the total twenty-one identified loci were located to chromosome positions where at least one QTL have been previously identified in other wheat genotype(s). The remaining eight QTLs are new which have been identified for the first time in this study. Pedigree analysis traced several known donors of PHS resistance in AAC Tenacious genealogy. Comparative analyses of the genetic intervals of identified QTLs with that of already identified and cloned PHS resistance gene intervals using IWGSC RefSeq v2.0 identified MFT-A1b (in QTL interval QPhs.lrdc-3A.1) and AGO802A (in QTL interval QPhs.lrdc-3A.2) on chromosome 3A, MFT-3B-1 (in QTL interval QPhs.lrdc-3B.1) on chromosome 3B, and AGO802D, HUB1, TaVp1-D1 (in QTL interval QPhs.lrdc-3D.1) and TaMyb10-D1 (in QTL interval QPhs.lrdc-3D.2) on chromosome 3D. These candidate genes are involved in embryo- and seed coat-imposed dormancy as well as in epigenetic control of dormancy. Conclusions: Our results revealed the complex PHS resistance genetics of AAC Tenacious and AAC Innova. AAC Tenacious possesses a great reservoir of important PHS resistance QTLs/genes supposed to be derived from different resources. The tracing of pedigrees of AAC Tenacious and other sources complements the validation of QTL analysis results. Finally, comparing our results with previous PHS studies in wheat, we have confirmed the position of several major PHS resistance QTLs and candidate genes. [ABSTRACT FROM AUTHOR]

IAC 2153 and IAC 2156 are new common bean cultivars with special bean grains for new markets, especially the international market. They have a mean hundred-seed weight of 50 g, mean cooking time of 32 min, resistance to anthracnose and Fusarium wilt, and moderate resistance to common bacterial blight. [ABSTRACT FROM AUTHOR]