Feedstock Development projects

Perennial Feedstock Genomics

This project applies genomic tools to identify useful genes, pathways, and germplasm for the development of perennial grasses as bioenergy feedstocks, with a focus on the Saccharinae.  Linkage mapping and association mapping is being conducted on inter- and intra-specific segregating populations and diversity panels of Sorghum, Saccharum, and Miscanthus.  Traits of fundamental interest include flowering phenology, rate and pattern of biomass accumulation, perenniality, and compositional variation.

project Highlights

2014 Highlights

We continued mapping plant height and flowering time QTL in partially isogenic populations. The current best candidate for a plant height QTL on chr9 (SbHt9.1) is a GA2-oxidase. The current best candidate for a linked flowering time QTL on chr9 (SbMa9.1) is a miR172a transcript. A Mendelian locus for midrib color on chr6 was fine-mapped. The current best candidate for this locus is a NAC transcription factor. We identified a stop codon in the first exon of this gene this is present in all recessive green midrib lines screened to date, and not present in any white midrib lines. We collected another season of biomass yield data in a panel of ~450 diverse photoperiod-sensitive sorghum accessions.

2013 Highlights

Sorghum was used as a model system to dissect the genetic control of traits relevant to bioenergy feedstock production. Over 2,000 diverse sorghum inbreds and six sorghum biparental populations were genotyped at ~100,000 single nucleotide polymorphisms and phenotyped for traits including plant height, flowering time, biomass yield, and sugar yield. We find that sorghum flowering time is controlled by Ghd7, a light- and clock-regulated gene that also controls flowering time variation in rice and maize. Ghd7 and related CCT-domain genes are strong candidates for flowering time variation in Saccharum and Miscanthus.

2012 Highlights

We genotyped 580 nearly isogenic pairs of tropical- and temperate-adapted sorghum lines (1,160 inbred lines) at ~50,000 SNPs to elucidate the genetic architecture of temperate adaptation in sorghum. Nearly isogenic pairs showed the highest genomic differentiation for the major plant height loci Dw1, Dw2, and Dw3, of which only Dw3 has been cloned. Nearly all of chromosome 6 differs between tropical and temperate-adapted pairs, apparently due to linkage between flowering time loci, of which only Ma1 has been cloned. We generated, phenotyped, and genotyped four segregating sorghum populations to fine-map these plant height and flowering time loci. Identification of these genes will broaden our genetic understanding of biomass accumulation in the Saccharinae, and will help guide genomics-assisted breeding efforts in sorghum and related feedstocks. In separate projects, we used association mapping to map loci with very large effects on two quantitative traits in sorghum: the accumulation of leaf wax, which is thought to improve drought tolerance, and the “juiciness” of sorghum stalks, which is important for sugar production in sweet sorghum.

2011 Highlights

Brown’s group characterized molecular variation in Sorghum, Saccharum, and Spartina populations using genotyping-by-sequencing and phenotyped diverse sorghum lines across three locations for maturity, biomass, and sugar accumulation.

2010 Highlights

Brown’s group conducted linkage and association mapping on inter- and intra-specific segregating populations and diversity panels completed of Sorghum, Saccharum, and Miscanthus. Next they will develop genotyping-by-sequencing (GBS) approaches to enable high-throughput genotyping of polyploids and intergeneric hybrids.

 

Publications

Published in 2014

Multi-Parental Mapping of Height and Flowering QTL in Partially-Isogenic Sorghum Populations, R. H. Higgins, C. S. Thurber, I. Assaranurak, Genes, Genomes, Genetics, V. 4, 1681-1687, pp. 1593-1602, June 11, 2014. 

 

Determining Sucrose and Glucose Levels in Dual-Purpose Sorghum Stalks by Fourier Transform Near Infrared (FT-NIR) Spectroscopy, S. F. Chen, M. G. Danao, P. J. Brown, Journal of the Science of Food and Agriculture, V. 94 (12), pp. 2569-2576, March 3, 2014. 

Published in 2013

Retrospective Genomic Analysis of Sorghum Adaptation to Temperate-Zone Grain Production, C. S. Thurber, J. M. Ma, R. H. Higgins, P. J. Brown, Genome Biology, 14(6), R68, doi: 10.1186/gb-2013-14-6-r68, June 28, 2013.

Published in 2012

Development of High-Density Genetic Maps for Barley and Wheat Using Genotyping-by-Sequencing, J. Poland, P. J. Brown, M. Sorrells, J-L Jannink. PLoS ONE 7: e32253.

 

Envisioning the Transition to a Next-Generation Biofuels Industry in the U.S. Midwest, I. Dweikat, C. Weil, S. Moose, L. Kochian, N. Mosier, K. Ileleji, P. J. Brown, W. Peer, A. Murphy, F. Taheripour, M. McCann, N. Carpita. Biofuels, Bioproducts & Biorefining 6: 376-386.

 

Population Genomic and Genome-wide Association Studies of Agroclimatic Traits in Sorghum, G. P. Morris, P. Ramu, S. P. Deshpande, C. T. Hash, T. Shah, H. D. Upadhyaya, O. Riera-Lizarazu, P. J. Brown, C. B. Acharya, S. E. Mitchell, J. Harriman, J. C. Glaubitz, E. S. Buckler, S. Kresovich. Proceedings of the National Academy of Sciences, 110: 453-458.

Published in 2011

Genetic Support for Phenotype-based Racial Classification in Sorghum, Patrick Brown, Sean Myles, Stephen Kresovich, Crop Sciences 51(1), pp. 224-230, doi:10.2135/cropsci2010.03.0179, 2011

 


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