Project description:Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world's poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8?M high-quality SNPs, 1.9?M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.
Project description:Nitrogen (N) fertilizers are a major agricultural input where more than 100 million tons are supplied annually. Cereals are particularly inefficient at soil N uptake, where the unrecovered nitrogen causes serious environmental damage. Sorghum bicolor (sorghum) is an important cereal crop, particularly in resource-poor semi-arid regions, and is known to have a high NUE in comparison to other major cereals under limited N conditions. This study provides the first assessment of genetic diversity and signatures of selection across 230 fully sequenced genes putatively involved in the uptake and utilization of N from a diverse panel of sorghum lines. This comprehensive analysis reveals an overall reduction in diversity as a result of domestication and a total of 128 genes displaying signatures of purifying selection, thereby revealing possible gene targets to improve NUE in sorghum and cereals alike. A number of key genes appear to have been involved in selective sweeps, reducing their sequence diversity. The ammonium transporter (AMT) genes generally had low allelic diversity, whereas a substantial number of nitrate/peptide transporter 1 (NRT1/PTR) genes had higher nucleotide diversity in domesticated germplasm. Interestingly, members of the distinct race Guinea margaritiferum contained a number of unique alleles, and along with the wild sorghum species, represent a rich resource of new variation for plant improvement of NUE in sorghum.
Project description:In the last decades, deficiency of macro- and micronutrients was considered as a serious problem associated with the increase in the human population. To meet the increased demand for food consumption, the wild relative plant might serve as an important source of new genetic material for increasing macro- and micronutrients. To investigate this, the variations in protein content, in vitro protein digestibility, tannin content, phytic acid content, total polyphenol content, and total and bioavailability of minerals were studied in grains of ten wild sorghums and two released sorghum cultivars. The results showed significant differences (p ≤ 0.05) in all quality tests among the genotypes. The highest percentage of total protein contents and in vitro protein digestibility were encountered in the grains of PQ-434 (14.6%) and the released cultivar AG8 (49.8%), respectively, while the highest concentrations of total and bioavailable iron were found in the grains of Almahkara (3.17 mg/100 g) and Abusabiba (92.8 mg/100 g), respectively. The grains of wild sorghum genotype Adar Umbatikh grains were found to possess higher total zinc contents. The PCA identified only five components of eigenvalues greater than one and cumulatively accounted for 88% of the total variation. It could be concluded that Almahkara and PQ-434 could be used as potential sources for iron and protein sorghum biofortification, respectively. Results from this study might be used in the development of new value-added products from wild sorghum grains by-products.
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
Project description:The AZ and NAZ of the materials that were loss of shattering (DZ129) and easy to shattering (W517) were used to perform RNA-Seq, and high-quality differential expression profiles were obtained.
Project description:Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels are not well understood and poorly predicted. Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.
Project description:Laccase is a key enzyme in plant lignin biosynthesis as it catalyzes the final step of monolignols polymerization. Sweet sorghum [Sorghum bicolor (L.) Moench] is considered as an ideal feedstock for ethanol production, but lignin greatly limits the production efficiency. No comprehensive analysis on laccase has ever been conducted in S. bicolor, although it appears as the most promising target for engineering lignocellulosic feedstock. The aim of our work is to systematically characterize S. bicolor laccase gene family and to identify the lignin-specific candidates. A total of twenty-seven laccase candidates (SbLAC1-SbLAC27) were identified in S. bicolor. All SbLACs comprised the equivalent L1-L4 signature sequences and three typical Cu-oxidase domains, but exhibited diverse intron-exon patterns and relatively low sequence identity. They were divided into six groups by phylogenetic clustering, revealing potential distinct functions, while SbLAC5 was considered as the closest lignin-specific candidate. qRT-PCR analysis deciphered that SbLAC genes were expressed preferentially in roots and young internodes of sweet sorghum, and SbLAC5 showed high expression, adding the evidence that SbLAC5 was bona fide involved in lignin biosynthesis. Besides, high abundance of SbLAC6 transcripts was detected, correlating it a potential role in lignin biosynthesis. Diverse cis regulatory elements were recognized in SbLACs promoters, indicating putative interaction with transcription factors. Seven SbLACs were found to be potential targets of sbi-miRNAs. Moreover, putative phosphorylation sites in SbLAC sequences were identified. Our research adds to the knowledge for lignin profile modification in sweet sorghum.
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
Project description:Gene variants leading to insertions or deletions of amino acid residues (indels) often have detrimental consequences for the folding of the encoded protein. Yet at some positions indels are tolerated or only result in partial unfolding. Typically unfolded proteins are targeted for protein quality control (PQC) degradation via ubiquitin-proteasome system, which in yeast is mediated by specific E3 ubiquitin-protein ligases, including Ubr1 and San1. Here we systematically probed the folding of a library of indel variants in the DHFR protein using sensitive yeast-based protein folding reporter. We show that deletion of Ubr1 and San1 leads to a greater fraction of folded DHFR indel variants, primarily positioned towards the N- and C-termini regions in DHFR. Intriguingly, most of the DHFR indels that are structurally stabilized in the E3 knockout strains, are also stabilized at lowered temperatures and upon binding the DHFR inhibitor methotrexate. This suggests that blocking PQC degradation can restore function to partially unfolded hypomorph variants, thus providing a potential therapeutic avenue for protein misfolding diseases.