Identification of two novel waxy alleles and development of their molecular markers in sorghum

Molecular insights on the origin and development of waxy genotypes in major crop plants

Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.

Crop Evolution of Foxtail Millet

Studies on the domestication, genetic differentiation, and crop evolution of foxtail millet are reviewed in this paper. Several genetic studies were carried out to elucidate the genetic relationships among foxtail millet accessions originating mainly from Eurasia based on intraspecific hybrid pollen semi-sterility, isozymes, DNA markers, and single-nucleotide polymorphisms. Most studies suggest that China is the center of diversity of foxtail millet, and landraces were categorized into geographical groups. These results indicate that this millet was domesticated in China and spread over Eurasia, but independent origin in other regions cannot be ruled out. Furthermore, the evolution of genes was reviewed (i.e., the Waxy gene conferring amylose content in the endosperm, the Si7PPO gene controlling polyphenol oxidase, the HD1 and SiPRR37 genes controlling heading time, the Sh1 and SvLes1 genes involved in grain shattering, and the C gene controlling leaf sheath pigmentation), and the variation and distribution of these genes suggested complex patterns of evolution under human and/or natural selection.

Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding

Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.

Amplification Refractory Mutation System (ARMS)-PCR for Waxy Sorghum Authentication with Single-Nucleotide Resolution

Waxy sorghum has greater economic value than wild sorghum in relation to their use in food processing and the brewing industry. Thus, the authentication of the waxy sorghum species is an important issue. Herein, a rapid and sensitive Authentication Amplification Refractory Mutation System-PCR (aARMS-PCR) method was employed to identify sorghum species via its ability to resolve single-nucleotide in genes. As a proof of concept, we chose a species of waxy sorghum containing the wx^c mutation which is abundantly used in liquor brewing. The aARMS-PCR can distinguish non-wx^c sorghum from wx^c sorghum to guarantee identification of specific waxy sorghum species. It allowed to detect as low as 1% non-wx^c sorghum in sorghum mixtures, which ar one of the most sensitive tools for food authentication. Due to its ability for resolving genes with single-nucleotide resolution and high sensitivity, aARMS-PCR may have wider applicability in monitoring food adulteration, offering a rapid food authenticity verification in the control of adulteration.

Waxy allele diversification in foxtail millet (Setaria italica) landraces of Taiwan

Foxtail millet (Setaria italica (L.) P. Beauv.), the second most cultivated millet species, is well adapted to diverse environments and remains an important cereal food and forage crop in arid and semiarid regions worldwide. A symbolic crop for indigenous Austronesian peoples, foxtail millet has been cultivated in Taiwan for more than 5,000 years, and landraces reflect diversifying selection for various food applications. A total of 124 accessions collected within Taiwan were assessed for Wx genotypes. Four identified Wx alleles, I, III, IV, and IX were caused by insertion of various transposable elements (TEs) and resulted in endosperm with non-waxy, low amylose content (AC), and waxy, respectively. A total of 16.9%, 4.0%, 49.2%, and 29.8% of accessions were classified as type I, III, IV, and IX, respectively; approximately half of the accessions belonged to the waxy type, indicating that glutinous grains were favored for making traditional food and wine. The TE insertion affected splicing efficiency rather than accuracy, leading to significantly reduced expression of wx in types III, IV, and IX, although their transcripts were the same as wild-type, type I. Consequently, the granule-bound starch synthase I (GBSSI) contents of the three mutated genotypes were relatively low, leading to waxy or low AC endosperm, and the Wx genotypes could explain 78% of variance in AC. The geographic distribution of Wx genotypes are associated with culinary preferences and migration routes of Taiwanese indigenous peoples-in particular, the genotype of landraces collected from Orchid Island was distinct from those from Taiwan Island. This information on the major gene regulating starch biosynthesis in foxtail millet endosperm can be applied to breeding programs for grain quality, and contributes to knowledge of Austronesian cultures.

Comparison of Physicochemical Characteristics of Starch Isolated from Sweet and Grain Sorghum

The worldwide interest about sweet sorghum (Sorghum bicolorL. Moench) goes towards stem sugar, but little has been focused on its grain. The starches were isolated from the grains of eight sweet and four grain sorghum varieties, and their physical, chemical, and morphological properties were carefully compared. The results reflected that starch from sweet varieties usually had larger granule size than that from grain ones, especially from two sweet varieties GL-4 and GL-6 with the granule size of 15.49 μm and 15.67 μm, respectively. The amylose content of sweet varieties starch was lower than that of grain ones. For water solubility index, starch from sweet varieties ranked top, whereas that from grain varieties ranked top for swelling power. The starch from both sweet and grain had A-type crystalline pattern, while the data from13C NMR reflected pattern differences forC1andC6resonance between sweet and grain varieties. Chains length distribution from sweet varieties debranched starch was found a little different from grain one. The starch particles surface of sweet sorghum was smooth with some dents, while that from grain was smooth without appearance of dents. As sweet sorghum has ability to withstand harsh environments where other crops do not and is characterized by low production cost, the extensive potential existed for starch from sweet varieties to be used in starch industries.

Effect of waxy (Low Amylose) on Fungal Infection of Sorghum Grain

Loss of function mutations in waxy, encoding granule bound starch synthase (GBSS) that synthesizes amylose, results in starch granules containing mostly amylopectin. Low amylose grain with altered starch properties has increased usability for feed, food, and grain-based ethanol. In sorghum, two classes of waxy (wx) alleles had been characterized for absence or presence of GBSS: wx(a) (GBSS(-)) and wx(b) (GBSS(+), with reduced activity). Field-grown grain of wild-type; waxy, GBSS(-); and waxy, GBSS(+) plant introduction accessions were screened for fungal infection. Overall, results showed that waxy grains were not more susceptible than wild-type. GBSS(-) and wild-type grain had similar infection levels. However, height was a factor with waxy, GBSS(+) lines: short accessions (wx(b) allele) were more susceptible than tall accessions (undescribed allele). In greenhouse experiments, grain from accessions and near-isogenic wx(a), wx(b), and wild-type lines were inoculated with Alternaria sp., Fusarium thapsinum, and Curvularia sorghina to analyze germination and seedling fitness. As a group, waxy lines were not more susceptible to these pathogens than wild-type, supporting field evaluations. After C. sorghina and F. thapsinum inoculations most waxy and wild-type lines had reduced emergence, survival, and seedling weights. These results are valuable for developing waxy hybrids with resistance to grain-infecting fungi.

Development of a waxy gene real-time PCR assay for the quantification of sorghum waxy grain in mixed cereal products

Background

Waxy-grain sorghum is used in most of the commercial cereal products in Korea. Worldwide, three waxy mutant alleles have been identified in the sorghum germplasm, and DNA markers for these alleles have been developed to identify the waxy genotype. However, that detection method cannot be used to determine the proportion of waxy content in samples containing both waxy and non-waxy sorghum. This study developed an assay that can be used to detect and quantify the waxy content of mixed cereal samples.

Results

All Korean waxy-grain sorghum used in this study contained the wx^a allele, and one wx^a allele-containing individual was also heterozygous for the wx^c allele. No individuals possessed the wx^b allele. The genotyping results were confirmed by iodine staining and amylose content analysis. Based on the sequence of the wx^a allele, three different types of primers (wx^a allele-specific, non-waxy allele-specific, and nonspecific) were designed for a quantitative real-time PCR (qPCR) assay; the primers were evaluated for qPCR using the following criteria: analytical specificity, sensitivity and repeatability. Use of this qPCR assay to analyze mixed cereal products demonstrated that it could accurately detect the waxy content of samples containing both waxy and non-waxy sorghum.

Conclusions

We developed a qPCR assay to identify and quantify the waxy content of mixed waxy and non-waxy sorghum samples as well as mixtures of cereals including sorghum, rice and barley. The qPCR assay was highly specific; the allele-specific primers did not amplify PCR products from non-target templates. It was also highly sensitive, detecting a tiny amount (>0.5%) of waxy sorghum in the mixed samples; and it was simple and repeatable, implying the robust use of the assay.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-015-0134-z) contains supplementary material, which is available to authorized users.