Abstract
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.
Highlights
Sorghum bicolor, a versatile and resilient C4 grass, is an important staple cereal in semiarid areas of Africa and Asia (Paterson et al, 2009)
We fine‐map the sorghum D locus to a four‐gene interval that includes two genes expressed in midrib tissue: a NAC transcription factor with a premature stop codon in the dd sorghum reference genome (Sobic.006G147400), and a threonine aldolase (Sobic.006G147600)
Threonine aldolase controls the catabolism of threonine to glycine and acetaldehyde, and Arabidopsis homologs THA1 and THA2 are both expressed in vascular tissue. tha1-2 mutants show dramatic increases in seed threonine content, whereas tha2-1 mutants have a lethal albino seedling phenotype(Joshi, Laubengayer, Schauer, Fernie, & Jander, 2006)
Summary
A dominant white midrib allele (D) was introduced into a genetic male sterile (ms3/ms3) version of Tx623, which carries a recessive green midrib allele (d), through four generations of backcrossing. For sugar yield measurements, paired rows of NILs were planted in six replicates at a single location in Urbana, IL in summer 2014, and phenotyped as previously described (Burks et al, 2015). For grain and stalk dry matter and moisture measurements, paired 2‐row plots of NILs were planted in four replicates at each of two locations (Urbana and Savoy, IL), and samples were pooled from 2‐6 individual representative plants per row for each time point. Midrib color in the GWAS panel was phenotyped as a binary trait (green vs white, Supporting information Table S7) in the youngest leaf at ~45 days after planting. The full length sequence of SbNAC074a from the DD NIL, which doesn't have the null mutation, was BLASTED in UNIPROT (http://www.uni prot.org) and homologs from Arabidopsis thaliana (sequence version 1), Oryza sativa subsp. RNAseq reads for this project have been deposited at the Illinois Data Bank (https://databank.illinois.edu/)
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