A sorghum NAC gene is associated with variation in biomass properties and yield potential

Xia, Jingnu; Zhao, Yunjun; Burks, Payne; Pauly, Markus; Brown, Patrick J.

doi:10.1002/pld3.70

Title: A sorghum NAC gene is associated with variation in biomass properties and yield potential

Journal Article · 23 July 2018 · Plant Direct

DOI: https://doi.org/10.1002/pld3.70 · OSTI ID:1461217

Xia, Jingnu ^[1]; Zhao, Yunjun ^[2]; Burks, Payne ^[1]; Pauly, Markus ^[2]; Brown, Patrick J. ^[1]

Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Crop Sciences
Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology

Sorghum bicolor is a C₄ grass widely cultivated for grain, forage, sugar, and biomass. The sorghum Dry Stalk (D) locus controls a qualitative difference between juicy green (dd) and dry white (D–) stalks and midribs, and co–localizes with a quantitative trait locus for sugar yield. Here, we apply fine–mapping and genome–wide association study (GWAS) to identify a candidate gene underlying D, and use nearly isogenic lines (NILs) to characterize the transcriptional, compositional, and agronomic effects of variation at the D locus. The D locus was fine–mapped to a 36 kb interval containing four genes. One of these genes is a NAC transcription factor that contains a stop codon in the NAC domain in the recessive (dd) parent. Allelic variation at D affects grain yield, sugar yield, and biomass composition in NILs. Green midrib (dd) NILs show reductions in lignin in stalk tissue and produce higher sugar and grain yields under well–watered field conditions. Increased yield potential in dd NILs is associated with increased stalk mass and moisture, higher biomass digestibility, and an extended period of grain filling. Transcriptome profiling of midrib tissue at the 4–6 leaf stages, when NILs first become phenotypically distinct, reveals that dd NILs have increased expression of a miniature zinc finger (MIF) gene. MIF genes dimerize with and suppress zinc finger homeodomain (ZF–HD) transcription factors, and a ZF–HD gene is associated with midrib color variation in a GWAS analysis across 1,694 diverse sorghum inbreds. A premature stop codon in a NAC gene is the most likely candidate polymorphism underlying the sorghum D locus. More detailed understanding of the sorghum D locus could help improve agronomic potential in cereals.

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Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0012400; DE‐SC0012400

OSTI ID:: 1461217

Alternate ID(s):: OSTI ID: 1461218; OSTI ID: 1575207; OSTI ID: 1575208

Journal Information:: Plant Direct, Vol. 2, Issue 7; ISSN 2475-4455

Publisher:: Wiley and American Society of Plant Biologists and Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 29 works

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Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice Fang, Yujie; You, Jun; Xie, Kabin Molecular Genetics and Genomics, Vol. 280, Issue 6 https://doi.org/10.1007/s00438-008-0386-6	journal	September 2008
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Grass Meristems I: Shoot Apical Meristem Maintenance, Axillary Meristem Determinacy and the Floral Transition Pautler, Michael; Tanaka, Wakana; Hirano, Hiro-Yuki Plant and Cell Physiology, Vol. 54, Issue 3 https://doi.org/10.1093/pcp/pct025	journal	February 2013
Multiple Classes of Transcription Factors Regulate the Expression of VASCULAR-RELATED NAC-DOMAIN7, a Master Switch of Xylem Vessel Differentiation Endo, Hitoshi; Yamaguchi, Masatoshi; Tamura, Taizo Plant and Cell Physiology, Vol. 56, Issue 2 https://doi.org/10.1093/pcp/pcu134	journal	September 2014
The Xylem and Phloem Transcriptomes from Secondary Tissues of the Arabidopsis Root-Hypocotyl Zhao, Chengsong; Craig, Johanna C.; Petzold, H. Earl Plant Physiology, Vol. 138, Issue 2 https://doi.org/10.1104/pp.105.060202	journal	May 2005
SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers of Arabidopsis Zhong, Ruiqin; Demura, Taku; Ye, Zheng-Hua The Plant Cell, Vol. 18, Issue 11 https://doi.org/10.1105/tpc.106.047399	journal	November 2006
WGCNA: an R package for weighted correlation network analysis Langfelder, Peter; Horvath, Steve BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-559	journal	December 2008
CONSTANS is a photoperiod regulated activator of flowering in sorghum Yang, Shanshan; Weers, Brock D.; Morishige, Daryl T. BMC Plant Biology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2229-14-148	journal	January 2014
EIN3 and ORE1 Accelerate Degreening during Ethylene-Mediated Leaf Senescence by Directly Activating Chlorophyll Catabolic Genes in Arabidopsis Qiu, Kai; Li, Zhongpeng; Yang, Zhen PLOS Genetics, Vol. 11, Issue 7 https://doi.org/10.1371/journal.pgen.1005399	journal	July 2015
Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach Poland, Jesse A.; Brown, Patrick J.; Sorrells, Mark E. PLoS ONE, Vol. 7, Issue 2 https://doi.org/10.1371/journal.pone.0032253	journal	February 2012
The Genetic Architecture of Maize Stalk Strength Peiffer, Jason A.; Flint-Garcia, Sherry A.; De Leon, Natalia PLoS ONE, Vol. 8, Issue 6 https://doi.org/10.1371/journal.pone.0067066	journal	June 2013
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline Glaubitz, Jeffrey C.; Casstevens, Terry M.; Lu, Fei PLoS ONE, Vol. 9, Issue 2 https://doi.org/10.1371/journal.pone.0090346	journal	February 2014
Variation in Biomass Composition Components among Forage, Biomass, Sorghum-Sudangrass, and Sweet Sorghum Types Stefaniak, Thomas R.; Dahlberg, Jeffery A.; Bean, Brent W. Crop Science, Vol. 52, Issue 4 https://doi.org/10.2135/cropsci2011.10.0534	journal	January 2012
Transcriptional Regulation of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up with Arabidopsis thaliana Handakumbura, Pubudu P.; Hazen, Samuel P. Frontiers in Plant Science, Vol. 3 https://doi.org/10.3389/fpls.2012.00074	journal	January 2012
NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants Nakano, Yoshimi; Yamaguchi, Masatoshi; Endo, Hitoshi Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00288	journal	May 2015
NAC Transcription Factors in Senescence: From Molecular Structure to Function in Crops Podzimska-Sroka, Dagmara; O'Shea, Charlotte; Gregersen, Per Plants, Vol. 4, Issue 3 https://doi.org/10.3390/plants4030412	journal	July 2015
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Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants Swarts, Kelly; Li, Huihui; Romero Navarro, J. Alberto The Plant Genome, Vol. 7, Issue 3 https://doi.org/10.3835/plantgenome2014.05.0023	journal	January 2014

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A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism Cooper, Elizabeth A.; Brenton, Zachary W.; Flinn, Barry S. BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5734-x	journal	May 2019
Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection Cuevas, Hugo E.; Prom, Louis K. BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6489-0	journal	January 2020
Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement Li, Yin; Tu, Min; Feng, Yaping Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1612-7	journal	November 2019
Correction to: Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement Li, Yin; Tu, Min; Feng, Yaping Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1621-6	journal	December 2019

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Title: A sorghum NAC gene is associated with variation in biomass properties and yield potential

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