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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #318936

Research Project: Genetic Enhancement of Sorghum as a Versatile Crop

Location: Plant Stress and Germplasm Development Research

Title: Translational genomics and marker assisted selection in sorghum case study using brown midrib (bmr) trait

Author
item Chopra, Ratan
item Burow, Gloria
item Sattler, Scott
item Acosta-martinez, Veronica
item Hayes, Chad
item Burke, John
item Xin, Zhanguo
item Emendack, Yves - Orise Fellow

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 8/6/2015
Publication Date: 9/1/2015
Citation: Chopra, R., Burow, G.B., Sattler, S.E., Acosta Martinez, V., Hayes, C.M., Burke, J.J., Xin, Z., Emendack, Y. 2015. Translational genomics and marker assisted selection in sorghum case study using brown midrib (bmr) trait [abstract]. Sorghum Improvement Conference of North America, September 1-3, 2015, Manhattan, Kansas. p. 1.

Interpretive Summary:

Technical Abstract: Translational genomics is a critical phase in harnessing the rich genomic data available for sorghum. There is a need to transform nucleotide variation data between sorghum germplasm such as that derived from RNA seq, genotype by sequencing (gbs) or whole genome resequencing thru translation and validation of Single Nucleotide Polymorphism (SNP) into easy access DNA markers for molecular and marker assisted breeding. Here, we use genes for lignin biosynthesis and the brown midrib phenotype, an important trait, which is associated with reduced lignin content as a case study for translational genomics. In this study SNP markers were developed from previously identified mutations in monolignol biosynthetic genes that affect the lignin content. In sorghum, there are three genes - caffeic acid O-methyltransferase (COMT), cinnamyl alcohol dehydrogenase (CAD) and 4-coumaroyl CoA ligase (4CL) that when mutated lowered the lignin content and produce the brown midrib phenotype. Twenty mutations are known in these three genes and nineteen of them were converted into SNP molecular markers that can easily be assayed using endpoint genotyping technology. The SNP markers were assayed in a pool of germplasm, which consisted of commercial varieties, bmr6-ref and bmr12-ref inbred lines and 6 new bmr mutants from EMS populations. We observed that the 6 new bmr mutants did not contain any of the known natural or induced mutations in three genes, which suggests the presence of new mutations in monolignol biosynthetic genes causing bmr phenotype. The SNP molecular markers for bmr described here provide a platform to screen for the variations present in diverse lines and provide an opportunity to identify new alleles for crop improvement.