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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

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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 three cloned Bmr loci encode genes involved in the monolignol biosynthetic pathway. There are eight known bmr loci in sorghum, but the two widely known are bmr6 and bmr12. A number of sorghum cultivars are referred to as bmr, but there is limited information as to their specific grouping, and it is important that new bmr lines in the pipeline can be easily genetically characterized. Hence, this study was performed to translate the genetic and DNA sequence information for bmr6 and bmr12, for use in the biomarker technology of single-nucleotide polymorphisms (SNPs). Through an analysis of variation for the two bmr genes, DNA markers in the form of cleave amplified polymorphic sequence (CAPS) and Kompetitive Allelele Specific Polymerase chain reaction (KASP) SNP markers were developed. The utility of the DNA markers for rapid and accurate identification of bmr6 or 12 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 evaluated and found to positively identify lines that harbor the different bmr genes. Fifteen KASP SNP markers (six for bmr6 and nine for bmr12) were developed and utilized for allelic discrimination and selection of bmr individuals at the seedling stage. The KASP marker bmr6-132  positively identified bmr6-ref  allele among materials evaluated and individuals of segregating F2 population at the seedling stage. The KASP DNA marker bmr12-129, positively identified germplasm among materials evaluated and individuals of the F2 population at the seedling stage to select plants that carry the  bmr12-ref allele . Results from this study also 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 and deployment of molecular information into specific CAPS and KASP DNA markers that are easy to access and can be applied in a breeding program, for use in efficient marker-assisted selection of bmr in sorghum.

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Acknowledgments

The technical support of Ms. Halee Hughes, John Peters and Jonanthan Vu are acknowledged.

Funding

United Sorghum Checkoff program provided funding through the project: “Genetic Enhancement of Sorghums” and the Ogallala Aquifer Program.

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Author notes

  1. Ratan Chopra

    Present address: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA

Authors and Affiliations

  1. Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, 3810 4th St, Lubbock, TX, 79415, USA

    Gloria Burow, Ratan Chopra, John Burke & Zhanguo Xin

  2. Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA

    Scott Sattler

  3. Wind Erosion and Water Conservation Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA

    Veronica Acosta-Martinez

Authors
  1. Gloria Burow
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  2. Ratan Chopra
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  4. John Burke
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  5. Veronica Acosta-Martinez
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  6. Zhanguo Xin
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Correspondence to Gloria Burow.

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ESM 1

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Supplementary Fig. 1

Phenotype of midribs from sorghum leaves collected from the germplasm analyzed in the study. Reference lines are shown in panels a through d: a=BTx399 (WT=non bmr); b=BN603 (bmr6 ref); c=BN604 (bmr12 ref); d=BN612 (bmr6/bmr12 ref). Commercial cultivars tested are shown in panels e to i: e=NK300; f=SP1990; g=GA340bmr; h=BK bmr; i=PSbmr. Panels j through n display the nonbmr BTx623 (j); subset of new mutants: AIMS bmr12 (k); new mutant AIMS-MUT525 (l); AIMS-MUT534 (m); AIMS-25M2-026 (n). (PNG 117 kb)

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Burow, G., Chopra, R., Sattler, S. et al. 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. Mol Breeding 39, 115 (2019). https://doi.org/10.1007/s11032-019-1010-7

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