No abstract

A key step during crop domestication is the loss of seed shattering. Here we show that seed shattering in sorghum is controlled by a single gene, Shattering1 (Sh1), which encodes a YABBY transcription factor. Domesticated sorghums harbor three different mutations at the Sh1 locus. Variants at regulatory sites in the promoter and intronic regions lead to a low level of expression, a 2.2-kb fragment deletion causes a truncated transcript that lacks the second and third exons, and a GT-to-GG splicing variant in the intron 4 results in removal of the exon 4. The distributions of these non-shattering haplotypes among sorghum landraces suggest three independent origins. The function of the rice ortholog (OsSh1) was subsequently validated with a shattering resistant mutant, and two maize orthologs (ZmSh1-1 and ZmSh1-5.1+ZmSh1-5.2) were verified with a large mapping population. Our results indicate that Sh1 genes for seed shattering were under parallel selection during sorghum, rice, and maize domestication.

Sorghum, an ancient old-world cereal grass, is the dietary staple of over 500 million people in more than 30 countries in the tropics and semitropics. Its C4 photosynthesis, drought resistance, wide adaptation, and high nutritional value hold the promise to alleviate hunger in Africa. Not present in other major cereals, such as rice, wheat, and maize, condensed tannins (proanthocyanidins) in the pigmented testa of some sorghum cultivars have been implicated in reducing protein digestibility but recently have been shown to promote human health because of their high antioxidant capacity and ability to fight obesity through reduced digestion. Combining quantitative trait locus mapping, meta-quantitative trait locus fine-mapping, and association mapping, we showed that the nucleotide polymorphisms in the Tan1 gene, coding a WD40 protein, control the tannin biosynthesis in sorghum. A 1-bp G deletion in the coding region, causing a frame shift and a premature stop codon, led to a nonfunctional allele, tan1-a. Likewise, a different 10-bp insertion resulted in a second nonfunctional allele, tan1-b. Transforming the sorghum Tan1 ORF into a nontannin Arabidopsis mutant restored the tannin phenotype. In addition, reduction in nucleotide diversity from wild sorghum accessions to landraces and cultivars was found at the region that codes the highly conserved WD40 repeat domains and the C-terminal region of the protein. Genetic research in crops, coupled with nutritional and medical research, could open the possibility of producing different levels and combinations of phenolic compounds to promote human health.domestication | food production | gene cloning | health benefit | natural selection

The 7.4 million plant accessions in gene banks are largely underutilized due to various resource constraints, but current genomic and analytic technologies are enabling us to mine this natural heritage. Here we report a proof-of-concept study to integrate genomic prediction into a broad germplasm evaluation process. First, a set of 962 biomass sorghum accessions were chosen as a reference set by germplasm curators. With high throughput genotyping-by-sequencing (GBS), we genetically characterized this reference set with 340,496 single nucleotide polymorphisms (SNPs). A set of 299 accessions was selected as the training set to represent the overall diversity of the reference set, and we phenotypically characterized the training set for biomass yield and other related traits. Cross-validation with multiple analytical methods using the data of this training set indicated high prediction accuracy for biomass yield. Empirical experiments with a 200-accession validation set chosen from the reference set confirmed high prediction accuracy. The potential to apply the prediction model to broader genetic contexts was also examined with an independent population. Detailed analyses on prediction reliability provided new insights into strategy optimization. The success of this project illustrates that a global, cost-effective strategy may be designed to assess the vast amount of valuable germplasm archived in 1,750 gene banks.

In crop species, adaptation to different agroclimatic regions creates useful variation but also leads to unwanted genetic correlations. Bouchet.......

Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production.heterosis | repulsion linkage | pseudo-overdominance | plant height | genome-wide association studies

Sweet sorghum has the potential to become a versatile feedstock for large-scale bioenergy production given its sugar from stem juice, cellulose/hemicellulose from stalks, and starch from grain. However, for researchers to maximize its feedstock potential a first step includes additional evaluations of the 2,180 accessions with varied origins in the US historic sweet sorghum collection. To assess genetic diversity of this collection for bioenergy breeding and population structure for association mapping, we selected 96 accessions and genotyped them with 95 simple sequence repeat markers. Subsequent genetic diversity and population structure analysis methods identified four subpopulations in this panel, which correlated well with the geographic locations where these accessions originated or were collected. Model comparisons for three quantitative traits revealed different levels of population structure effects on flowering time, plant height, and brix. Our results suggest that diverse germplasm accessions curated from different geographical regions should be considered for plant breeding programs to develop sweet sorghum cultivars or hybrids, and that this sweet sorghum panel can be further explored for association mapping.

Knowledge of the genetic bases of grain quality traits will complement plant breeding efforts to improve the end-use value of sorghum [Sorghum bicolor (L.) Moench]. Candidate gene association mapping was used on a diverse panel of 300 sorghum accessions to assess marker-trait associations for 10 grain quality traits measured using the single kernel characterization system (SKCS) and near-infrared refl ectance spectroscopy (NIRS). The analysis of the accessions through 1290 genomewide single nucleotide polymorphisms (SNPs) separated the panel into fi ve subpopulations that corresponded to three major sorghum races (durra, kafi r, and caudatum), one intermediate race (guinea-caudatum), and one working group (zerazera-caudatum). These subpopulations differed in kernel hardness, acid detergent fi ber, and total digestible nutrients. After model testing, association analysis between 333 SNPs in candidate genes and/or loci and grain quality traits resulted in eight signifi cant marker-trait associations. A SNP in starch synthase IIa (SSIIa) gene was associated with kernel hardness (KH) with a likelihood ratio-based R 2 (R LR 2 ) value of 0.08, a SNP in starch synthase (SSIIb) gene was associated with starch content with an R LR 2 value of 0.10, and a SNP in loci pSB1120 was associated with starch content with an R LR 2 value of 0.09.