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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Grain Quality and Structure Research » Research » Publications at this Location » Publication #407286
Research Project: Grain Composition Traits Related to End-Use Quality and Value of Sorghum

Location: Grain Quality and Structure Research

Title: An updated molecular toolkit for genomics - assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench]

Author
item YERKA, MELINDA - University Of Nevada
item LIU, ZHIYUAN - Texas Tech University
item Bean, Scott
item NIGAM, DEEPTI - Texas Tech University
item HAYES, CHAD - US Department Of Agriculture (USDA)
item DRUETTO, DIEGO - Richard Seeds, Ltc
item KRISHNAMOORTHY, GABRIEL - Richard Seeds, Ltc
item FANGMAN, SHELLEY - Richard Seeds, Ltc
item CUCIT, GONZALO - Nuseed
item ATIM, JACKIE - University Of California
item JIAO, YINPING - Texas Tech University

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2025
Publication Date: 8/11/2025
Citation: Yerka, M.K., Liu, Z., Bean, S.R., Nigam, D., Hayes, C., Druetto, D., Krishnamoorthy, G., Fangman, S., Cucit, G., Atim, J., Jiao, Y. 2025. An enhanced genome assembly and functional, high-throughput molecular markers enable genomics-assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench]. Euphytica. https://doi.org/10.1007/s13353-025-00993-1.
DOI: https://doi.org/10.1007/s13353-025-00993-1

Interpretive Summary: Specific types of sorghum germplasm contain genes that result in lower than normal levels of amylose, a specific type of starch found in the grain. These types of sorghum are referred to as "waxy." Waxy starch has unique properties and waxy sorghum would provide novel functionality for food, feed, and biofuel markets. However, some waxy sorghum varieties have been reported to have reduced yield and germination rates, which would potentially limit widespread adoption of such material. To help facilitate breeding efforts to develop improved waxy sorghum varieties, this project developed new genetic markers for the waxy trait and provides new molecular tools to help sorghum breeders and geneticists develop new waxy sorghum with improved agronomic properties.

Technical Abstract: Several mutations of the sorghum [Sorghum bicolor (L.) Moench] GRANULE-BOUND STARCH SYNTHASE (GBSS) gene [Sobic.010G022600] result in a low amylose:amylopectin starch ratio in the endosperm and confer a glutinous, “waxy” texture; hence, the wild-type gene is commonly referred to as Waxy (Wx). Numerous studies have characterized recessive waxy (wx) alleles for their ability to improve starch digestibility in ethanol production, human foods and beverages, and animal feed. The current study provides the most in-depth characterization to date of the Waxy locus for improved molecular breeding using next-generation sequencing approaches. An enhanced genome assembly was constructed from the Tx623 reference genome (v3.1.1) to include a 5.6 kb insertion that is causal of the wxa allele in chromosome 10. A large retrotransposon derivative (LARD) was identified in the insertion sequence. Inclusion of the insertion in the enhanced assembly improved read mapping of whole-genome sequence data at Sobic.010G022600 in wxa individuals, resulting in fewer broken reads in sequences flanking the insertion and the identification of 78 uniquely mapped reads in the genome. Functional PACE-PCR markers for Wx, wxa, and wxb alleles were developed and validated in three public and private breeding programs. The chromosome 10 reconstruction was uploaded to The Practical Haplotype Graph. These new molecular breeding resources will improve the efficiency of developing high-yielding, climate-smart waxy sorghum hybrids for end-uses in foods, feeds, and fuels.