Metabolic diversity in sorghum: Mechanism underlying grain color variation and fermentation quality

Key messageSeventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, and a new recessive allelic variant of TAN2 gene was discovered.Sorghum is mainly used for brewing distilled liquors in China. Since grain tannins play an important role in liquor brewing, accurately understanding the relationship between grain color and tannin content can provide basis for selection standards of tannin sorghum. We resequenced a panel of 242 Chinese sorghum accessions and performed population structure and genome-wide association study (GWAS) to identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, and tannin content. Phylogenetic analysis, principal component analysis (PCA), and admixture model were used to infer population structure. Two distinct genetic sub-populations were identified according to their corresponding northern and southern geographic origin. To investigate the genetic basis of natural variation in sorghum grain color, GWAS with 2,760,264 SNPs was conducted in four environments using multiple models (Blink, FarmCPU, GLM, and MLM). Seventy-three QTL were identified to be associated for the color of exocarp, mesocarp, testa, and tannin content on all chromosomes except chromosome 5, of which 47 might be novel QTL. Some important QTL were found to colocalize with orthologous genes in the flavonoid biosynthetic pathway from other plants, including orthologous of Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 and AT5G41220 (GST), as well as orthologous of rice (Oryza sativa) MYB61 and OsbHLH025. Our investigation of the variation in grain color and tannin content in Chinese sorghum germplasm may help guide future sorghum breeding for liquor brewing.

Genetic diversity analysis is an important component in conventional and marker-assisted breeding. The objective of this study was to assess the level of genetic diversity among 100 sorghum accessions, which were selected randomly from the Sorghum National Germplasm Bank maintained at Agricultural Research Council, South Africa. A total of 136 Kompetitive Allele-Specific PCR (KASP) markers were used in this study. The KASP markers were previously derived from single-nucleotide polymorphic (SNP) analysis of the world-wide sorghum accessions by other research groups. A total of 110 KASP markers were polymorphic and recorded an average polymorphic information content (PIC) value of 0.3, which indicated high level of discrimination of the markers. The markers had an average gene diversity and observed heterozygosity of 0.3 and 0.10, respectively. Analysis of molecular variance revealed a significantly high variation among accessions (83% and 89%) than within accessions (10% and 11%) based on breeding status and geographic origin, respectively. Genetic distance varied from 0.0 between SA0672 and SA0673, SA1282 and SA0670 to 0.57 between Hakika and SA1442 with an average mean of 0.30. The dendrogram and model-based population analysis identified three and four distinct groups in 95 sorghum accessions, respectively. These results imply the presence of genetic diversity and lack of genetic bottleneck within the National Sorghum Germplasm Bank, which could be highly relevant for sorghum breeding and germplasm maintenance

Evaluation of simplified water-crop yield models

Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The expected heterozygosity values ranged from 0.10 to 0.50 with an average of 0.32, while the average observed heterozygosity (0.15) was relatively low, which is a typical value for autogamous crops species like sorghum. Moderate polymorphic information content (PIC) values were identified with a mean of 0.26, which indicates the informativeness of the chosen SNP markers. The population structure and cluster analyses revealed four main clusters with a high level of genetic diversity among the accessions studied. The variation within populations (41.5%) was significantly higher than that among populations (30.8%) and between samples within the structure (27.7%). The study identified distantly related sorghum accessions such as SAMSORG 48, KAURA RED GLUME; Gadam, AS 152; CSRO1, ICNSL2014-062; and YALAI, KAFI MORI. The accessions exhibited wide genetic diversity that will be useful in developing new gene pools and novel genotypes for West Africa sorghum breeding programs.

BackgroundSorghum (Sorghum bicolor L. Moench) accumulates 3-deoxyanthocyanidins and exhibits orange to purple coloration on parts of the leaf in response to infection with the fungus Bipolaris sorghicola. We aimed to identify the key genes determining this color variation.ResultsSorghum populations derived from Nakei-MS3B and M36001 accumulated apigeninidin, or both apigeninidin and luteolinidin, in different proportions in lesions caused by B. sorghicola infection, suggesting that the relative proportions of the two 3-deoxyanthocyanidins determine color variation. QTL analysis and genomic sequencing indicated that two closely linked loci on chromosome 4, containing the flavonoid 3′-hydroxylase (F3′H) and Tannin1 (Tan1) genes, were responsible for the lesion color variation. The F3′H locus in Nakei-MS3B had a genomic deletion resulting in the fusion of two tandemly arrayed F3′H genes. The recessive allele at the Tan1 locus derived from M36001 had a genomic insertion and encoded a non-functional WD40 repeat transcription factor. Whole-mRNA sequencing revealed that expression of the fused F3′H gene was conspicuously induced in purple sorghum lines. The levels of expression of F3′H matched the relative proportions of apigeninidin and luteolinidin.ConclusionsExpression of F3′H is responsible for the synthesis of luteolinidin; the expression level of this gene is therefore critical in determining color variation in sorghum leaves infected with B. sorghicola.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-0500-7-761) contains supplementary material, which is available to authorized users.

The evolution of floral traits in animal-pollinated plants involves the interaction between flowers as signal senders and pollinators as signal receivers. Flower colors are very diverse, effect pollinator attraction and flower foraging behavior, and are hypothesized to be shaped through pollinator-mediated selection. However, most of our current understanding of flower color evolution arises from variation between discrete color morphs and completed color shifts accompanying pollinator shifts, while evidence for pollinator-mediated selection on continuous variation in flower colors within populations is still scarce. In this review, we summarize experiments quantifying selection on continuous flower color variation in natural plant populations in the context of pollinator interactions. We found that evidence for significant pollinator-mediated selection is surprisingly limited among existing studies. We propose several possible explanations related to the complexity in the interaction between the colors of flowers and the sensory and cognitive abilities of pollinators as well as pollinator behavioral responses, on the one hand, and the distribution of variation in color phenotypes and fitness, on the other hand. We emphasize currently persisting weaknesses in experimental procedures, and provide some suggestions for how to improve methodology. In conclusion, we encourage future research to bring together plant and animal scientists to jointly forward our understanding of the mechanisms and circumstances of pollinator-mediated selection on flower color.

The variation and inheritance of juvenile shell color and pigmentation pattern in the freshwater mussel, Hyriopsis cumingii, were reported in 1‐yr‐old progeny of eight families. There were three distinctive phenotypes of shell color and pigmentation patterns observed, including a greenish‐brown shell with radial rays, yellowish‐brown shell with radial rays, and yellowish‐brown shell without radial rays. There were no greenish‐brown individuals without radial rays. The shell color phenotypes showed variation with the growth in juvenile Stage I (1–3 cm in shell length), and the percentage of individuals with radial rays increased once they reached a shell length of 11 mm and then stabilized after reaching 20 mm in shell length. Shell color differentiation became more apparent at a shell length of 26 mm. Results of chi‐square tests of the segregation ratio of shell color or ray phenotypes obtained from eight families at juvenile Stage II (6–9 cm in shell length) suggested that greenish‐brown is controlled by a dominant allele (G) and yellowish‐brown‐shell phenotype is by a recessive allele (y); the ray pattern phenotype is controlled by a recessive (r) and a dominant allele (R) at a single locus. Shell color phenotypes may be a useful genetic marker for future selective breeding of triangle pearl mussels.

Decision letter: Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

Editor's evaluation: Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

The identification and analysis of allelic variation are important bases for crop diversity research, trait domestication and molecular marker development. Grain tannin content is a very important quality trait in sorghum. Higher tannin levels in sorghum grains are usually required when breeding varieties resistant to bird damage or those used for brewing liquor. Non-tannin-producing or low-tannin-producing sorghum accessions are commonly used for food and forage. Tan1 and Tan2, two important cloned genes, regulate tannin biosynthesis in sorghum, and mutations in one or two genes will result in low or no tannin content in sorghum grains. Even if sorghum accessions contain dominant Tan1 and Tan2, the tannin contents are distributed from low to high, and there must be other new alleles of the known regulatory genes or new unknown genes contributing to tannin production. The two parents 8R306 and 8R191 did not have any known recessive alleles for Tan1 and Tan2, and it was speculated that they probably both had dominant Tan1 and Tan2 genotypes. However, the phenotypes of two parents were different; 8R306 had tannins and 8R191 had non-tannins in the grains, so these two parents were constructed as a RIL population. Bulked segregant analysis (BSA) was used to determine other new alleles of Tan1 and Tan2 or new Tannin locus. Tan1 and Tan2 full-length sequences and tannin contents were detected in wild sorghum resources, landraces and cultivars. We identified two novel recessive tan1-d and tan1-e alleles and four recessive Tan2 alleles, named as tan2-d, tan2-e, tan2-f, and tan2-g. These recessive alleles led to loss of function of Tan1 and Tan2, and low or no tannin content in sorghum grains. The loss-of-function alleles of tan1-e and tan2-e were only found in Chinese landraces, and other alleles were found in landraces and cultivars grown all around the world. tan1-a and tan1-b were detected in foreign landraces, Chinese cultivars and foreign cultivars, but not in Chinese landraces. These results implied that Tan1 and Tan2 recessive alleles had different geographically distribution in the worldwide, but not all recessive alleles had been used in breeding. The discovery of these new alleles provided new germplasm resources for breeding sorghum cultivars for food and feed, and for developing molecular markers for low-tannin or non-tannin cultivar-assisted breeding in sorghum.

Sorghum is an important grain crop in many parts of the world, especially in dry regions. It is an important crop for food and feed, and its role in energy production is currently growing. In Ethiopia, sorghum is a multi-purpose crop used for many different functions such as fuel, housing and animal feed. Information on genetic diversity levels among and within sorghum accessions will increase the efficiency of the sorghum improvement programmes. Field experiments were conducted in Potchefstroom, South Africa, during the summer growing seasons of 2009 and 2010, to estimate the level of phenotypic diversity among 22 sorghum accessions. The experiment was laid out in a randomised complete block design with three replications. Nine qualitative and 20 quantitative morphological traits were recorded. Analysis of variance for the quantitative traits revealed that differences among accessions were highly significant for all traits. Qualitative traits diversity index values varied from 31% (panicle compactness and shape) to 84% (glume colour). The pair-wise genetic distances based on phenotypic traits showed varying genetic distances. Cluster analysis of the phenotypic traits resulted in four distinct groups of accessions with genetic distances ranging from 0.40 to 1.59. Therefore, the phenotypic markers provide a useful measure of genetic distances among sorghum accessions to identify potential donors or parental material for future breeding efforts.

For the fermentation of vinegar using onion, acetic acid bacteria and yeast strains with high fermentation ability were screened. Among them, Saccharomyces cerevisiae 1026 was selected as a starter for ethanol production and Acetobacter orientalis MAK88 was selected as a vinegar producer. When the two-stage fermentation of onion vinegar was performed at 28 °C, the titratable acidity reached 4.80% at 24 h of fermentation. When semi-continuous fermentation proceeded to charge-discharge consisting of three cycles, the acetic acid content reached 4.35% at 48 h of fermentation. At this stage, the fermentation efficiency, acetic acid productivity, and specific product formation rate were 76.71%, 17.73 g/(L·d), and 20.58 g/(g·h), respectively. The process in this study significantly reduced the fermentation time and simplified the vinegar production process. The content of total flavonoids and total polyphenols in onion vinegar were 104.36 and 455.41 μg/mL, respectively. The antioxidant activities of onion vinegar in terms of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic) acid (ABTS+) radical scavenging activity, and reducing power were 75.33%, 98.88%, and 1.28, respectively. The nitrite scavenging abilities of onion vinegar were 95.38 at pH 1.2. The onion vinegar produced in this study showed higher organoleptic acceptability than commercial onion vinegar.

BackgroundIn sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study.ResultsLevels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study.ConclusionPromising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.

Sorghum has great potential to be developed in marginal lands of Indonesia including East Nusa Tenggara. However, the information about sorghum diversity in this area was very limited. This research aimed to describe morphological variation, and assessing the value of genetic diversity based on morphological characters of local sorghum cultivar of East Nusa Tenggara. The exploration and sample collection were conducted in 3 islands, i.e.: Timor, Sumba, and Flores. The observation of morphological characters was based on sorghum descriptor. Morphological character similarities were analyzed using Simple Matching (SM) coefficient, and a dendrogram was constructed using Unweighted Pair Group Method with Arithmetic Average (UPGMA) method. The results showed that 36 accessions of sorghum in East Nusa Tenggara varied in 17 morphological characters. At the similarity coefficients of 48%, all sorghum accessions were separated into 2 groups based on the presence or absence of aleurone layer. Group I consisted of 12 accessions with no aleurone layer, while group II consisted of 24 accessions has aleurone layer. The genetic diversity of sorghum of East Nusa Tenggara is low (I=0.62–0.71 and h=0.37-0.42). The genetic diversity between populations (HT=0.4203) is higher than within populations (HS=0.3961). This study provides the first complete information about sorghum diversity in East Nusa Tenggara that will be useful as basic information for sorghum development in this area in the future.

Acetobacter pasteurianus JST-S was screened from solid fermented grains of vinegar in China, identified by molecular analysis, and used for the production of purple sweet potato vinegar using purple sweet potato as the substrate. By orthogonal experiment, maximum total acid concentration (4.26% [v/v]) was achieved under optimized conditions as follows: fermentation time, 3.5days; ethanol content, 9% v/v; and inoculum size, 8% v/v. During the production of purple potato vinegar, the anthocyanin concentration decreased from 652.07 to 301.73μg/mL. The antioxidant activity of products, including diphenyl-picryl hydrazide radical-scavenging capacity (above 60%), reducing power (above 0.47), and hydroxyl radical-scavenging capacity (above 46%), showed positive linear regression (P<0.01), which could be related with the changes in anthocyanin concentration and antioxidant activities at different stages of vinegar fermentation. The acetic acid and other non-phenolic antioxidants in purple sweet potato vinegar may have contributed to the antioxidant activities. Results of these studies may provide a reference for the industrial production of vinegar by liquid fermentation of purple sweet potato.