Molecular characterization and comparative analysis of two waxy alleles in barley

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.

Waxy and non-waxy barley cultivars exhibit differences in the targeting and catalytic activity of GBSS1a

Amylose synthesis is strictly associated with activity of granule-bound starch synthase (GBSS) enzymes. Among several crops there are cultivars containing starch types with either little or no amylose known as near-waxy or waxy. This (near) amylose-free phenotype is associated with a single locus (waxy) which has been mapped to GBSS-type genes in different crops. Most waxy varieties are a result of either low or no expression of a GBSS gene. However, there are some waxy cultivars where the GBSS enzymes are expressed normally. For these types, single nucleotide polymorphisms have been hypothesized to represent amino-acid substitutions leading to loss of catalytic activity. We here confirm that the HvGBSSIa enzyme from one such waxy barley variety, CDC_Alamo, has a 90% reduction in catalytic activity. We also engineered plants with expression of transgenic C-terminal green fluorescent protein-tagged HvGBSSIa of both the non-waxy type and of the CDC_Alamo type to monitor their subcellular localization patterns in grain endosperm. HvGBSSIa from non-waxy cultivars was found to localize in discrete concentric spheres strictly within starch granules. In contrast, HvGBSSIa from waxy CDC_Alamo showed deficient starch targeting mostly into unknown subcellular bodies of 0.5-3 µm in size, indicating that the waxy phenotype of CDC_Alamo is associated with deficient targeting of HvGBSSIa into starch granules.

Effect of wide variation of the Waxy gene on starch properties in hull-less barley from Qinghai-Tibet plateau in China

Granule-bound starch synthase I (GBSS I) plays an important role in the synthesis of amylose and in the determination of starch properties in barley grains. Genomic DNAs for the Waxy gene encoding GBSS I protein were sequenced from 34 barley accessions or lines from Qinghai-Tibet plateau in China, to identify Waxy gene nucleotide variations and study the roles of polymorphic sites of the Waxy gene on expression levels of Waxy transcripts and GBSS I proteins and on resulting starch properties. A total of 116 DNA polymorphic sites were identified within the barley Waxy gene, which divided the studied accessions into 11 haplotypes. Among 33 nucleotide polymorphic sites in coding regions, 5 SNPs in three exons were found to play different roles on the expression level of the Waxy transcript and the GBSS I protein and on the amylose content and starch properties. One SNP G(3935)-to-T substitution in the 10th exon in the accession Z999 (HP II-2) caused a high expression level of the Waxy transcript and the GBSS I protein and the amylose free phenotype. The other SNP alteration was a C(2453)-to-T in the fifth exon in the accession Z1191 (HP I-5), which drastically reduced the expression level of the Waxy transcript and the GBSS I protein and, finally, produced the amylose free phenotype. Three SNPs in the seventh exon in the accession Z1337 (HP I-6) did not significantly change the level of Waxy transcript, the GBSS I protein, and starch properties, except obviously reducing the breakdown value of starch viscosity and extending the peak time. A total of 84 DNA polymorphic sites were found in the noncoding regions. A 403 bp deletion at 5'UTR in the accession Z1979 (HP I-3) had low transcript level, low GBSS I protein level, and low amylose content due to the deletion of cis-acting DNA regulatory elements. A 191 bp insertion and a 15 bp insertion in the first intron and second exons, respectively, may be closely related to a higher transcript level of the Waxy gene and significant differences in some starch properties of the Waxy I DNA group as compared to the Waxy II DNA group. This study indicates the specific variations of the Waxy gene have a great effect on amylose synthesis and starch properties of hull-less barley, which could be very useful to produce new barley with variable starch properties.

Current perspectives and the future of domestication studies

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.

Characterization and expression analysis of waxy alleles in barley accessions

Granule Bound Starch Synthase I (GBSS I) encoded by the waxy gene plays an important role in accumulating amylose during the development of starch granules in barley. In this study, we isolated and characterized waxy alleles of three waxy (GSHO 908, GSHO 1828 and NA 40) and two non-waxy barley accessions (PI 483237 and CIho 15773), estimated the expression patterns of waxy genes via Real-time quantitative PCR (RT-qPCR), investigated promoter activity by analyzing promoter-GUS expression, and examined possible effects of waxy alleles on starch granule morphology in barley accessions by scanning electron microscopy (SEM). A 193-bp insertion in intron 1, a 15-bp insertion in the coding region, and some single nucleotide polymorphic sites were detected in the waxy barley accessions. In addition, a 397-bp deletion containing the TATA box, transcription starting point, exon 1 and partial intron 1 were also identified in the waxy barley accessions. RT-qPCR analysis showed that waxy accessions had lower waxy expression levels than those of non-waxy accessions. Transient expression assays showed that GUS activity driven by the 1,029-bp promoter of the non-waxy accessions was stronger than that driven by the 822-bp promoter of the waxy accessions. SEM revealed no apparent differences of starch granule morphology between waxy and non-waxy accessions. Our results showed that the 397-bp deletion identified in the waxy barley accessions is likely responsible for the reduction of waxy transcript, leading to lower concentrations of GBSS I protein thus lower amylose content.