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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 #345559
Title: Deployment of SNP (CAPS and KASP) markers for allelic discrimination and easy access to functional variants for brown midrib genes bmr6 and bmr12 in Sorghum bicolor

Author
item Burow, Gloria
item Chopra, Ratan
item Sattler, Scott
item Burke, John
item Acosta-Martinez, Veronica
item Xin, Zhanguo

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2019
Publication Date: 7/26/2019
Citation: Burow, G.B., Chopra, R., Sattler, S.E., Burke, J.J., Acosta Martinez, V., Xin, Z. 2019. Deployment of SNP (CAPS and KASP) markers for allelic discrimination and easy access to functional variants for brown midrib genes bmr6 and bmr12 in Sorghum bicolor. Molecular Breeding. 39:115. https://doi.org/10.1007/s11032-019-1010-7.
DOI: https://doi.org/10.1007/s11032-019-1010-7

Interpretive Summary: Translational genomics led to identification of robust and stable single nucleotide polymorphism (SNP) DNA markers for use in selection and breeding of brown midrib trait in forage and bioenergy sorghums. This study utilized genomic data for genes in the monolignol pathway to identify robust and stable SNP markers for two classes of brown midrib trait, an important trait which is associated with reduced lignin content and greater ethanol conversion efficiency. Specifically, the new kompetetive alleles specific polymerase (KASP) DNA markers for bmr6 and bmr12 provide a platform to screen for the variation in brown midrib trait at all stages of plant development for marker assisted selection and contribute to an opportunity to identify new alleles for improvement of forage and biomass sorghums.

Technical Abstract: The brown midrib (bmr) phenotype is a recessive trait of sorghum (Sorghum bicolor L. Moench) that results in overall lignin reduction and is associated with enhanced ruminant digestibility and increased feedstock to ethanol conversion efficiency. The molecular basis for bmr is attributed to the modifications of the phenyl-propanoid pathway. There are several classes of bmr, but the two widely known groups based on different genes that underpin the trait are: bmr6 and 12. bmr6 is due to inactivation of cinnamyl alcohol dehydrogenase (CAD) and bmr12 is due to alteration of caffeic acid O-methyltransferase (COMT). To translate the genetic and DNA sequence information for bmr6 and 12, for use in the biomarker technology of single nucleotide polymorphisms(SNPs), this study assembled reported variation for the two bmr genes and developed DNA markers in the form of cleave amplified polymorphic sequence (CAPS) and Kompetetive Allelele Specific Polymerase chain reaction (KASP) SNP markers. The utility of the DNA markers for rapid and accurate identification of bmr individuals at the seedling stage were validated in a group of sorghum germplasm and a genetic population through marker assisted selection. Two CAPS DNA markers, (one each for bmr6 and 12) were developed and found to positively identify lines that harbor the different bmr genes. Sixteen KASP SNP markers, (6 for bmr6 and 10 for bmr12) were developed and validated for marker assisted selection of bmr individuals at the seedling stage. The KASP marker, bmr6-132 positively identified bmr6 germplasm among materials evaluated and individuals of the population at the seedling stage. The KASP DNA marker bmr12-129, positively identified bmr12 germplasm among materials evaluated and individuals of the population at the seedling stage. Results from this study likewise classified two sorghum germplasm as bmr12 and these lines can be utilized as specific donor of this bmr class using marker assisted selection. This work demonstrated the successful translation of molecular information into specific DNA markers that are easy to access and apply in a breeding program, for use in efficient markers assisted selection of bmr in sorghum.