Genome-wide association mapping identifies an SNF4 ortholog that impacts biomass and sugar yield in sorghum and sugarcane

Abstract

Sorghum is feed/industrial crop in the developed countries and a staple food in the rest of the world. In this study, we evaluated the sorghum mini core (MC) collection for days to 50% flowering (DF), biomass (BM), plant height (PH), soluble solid content (SSC) and juice weight (JW) and the sorghum reference set (RS) for DF and PH in 7-12 testing environments and performed association mapping with 6,094,317 SNP markers in the MC and 265,500 SNPs for the RS. We identified in the MC panel three QTLs for DF, one for PH, one for BM, and two for JW. In the RS panel we identified another PH QTL on chromosome 6 also associated with DF, BM, JW, and SSC in the MC panel. Transgenic studies of three genes selected from the locus revealed that Sobic.006G061100 (SbSNF4-2) increased BM, SSC, JW, and PH when overexpressed in both sorghum and sugarcane and delayed flowering in transgenic sorghum. SbSNF4-2 encodes a γ subunit of the evolutionarily conserved AMPK/SNF1/SnRK1 heterotrimeric complexes and overexpression of human or mouse γ2 in heart or the whole body also increases heart or body biomass. SbSNF4-2 and its orthologs will be valuable in genetic enhancement of biomass and sugar yield in plants.

Genome-wide association study of plant color in Sorghum bicolor

“…To identify SNP markers linked to the trait, we used the following criteria: 1) more than one marker associated with plant color and at least one of the markers had −log 10 ( P ) higher than the threshold ( Upadhyaya et al., 2022 ), and 2) association had to be present across all three environments (2021_HN, 2022_HN, and 2022_FY). Based on these criteria, we identified eight loci distributed on chromosomes 1, 2, 4, 5, 6, and 9 ( Figure 2 ; Supplementary Figure S1 ; Table 1 ).…”

“…This panel has been extensively characterized, such as its genetic structure and linkage disequilibrium ( Wang et al., 2013 ) and effectiveness for association mapping ( Upadhyaya et al., 2013 ). Most importantly, the panel has been used to clone a pleiotropic SbSNF4-2 ( SnRK1βγ2 ) that increases both biomass and sugar yield in sorghum and sugarcane ( Upadhyaya et al., 2022 ). We scored leaf sheath/leaf color at maturity as tan, red, or purple across three testing environments in Tengqiao/Hainan and Fengyang/Anhui, China, performed association mapping with 6,094,317 SNP markers ( Wang et al., 2021 ), and identified candidate genes strongly linked to plant color.…”

Genetic architecture and molecular regulation of sorghum domestication

“…Three nonfunctional alleles were found in early-flowering accessions cultivated in long-day conditions, which indicates the possible multiple origins of photoperiod-insensitive sorghum in diversification progress when sorghum spreads to temperate regions. Another association analysis study of sorghum maturity also identified the SbPRR37 gene by using GWAS in a sorghum mini-core collection (Upadhyaya et al 2013). Multiple variant alleles of the SbPRR37 genomic sequence from 253 landraces and historic sorghum cultivars were found.…”

“…In 2001, Hart et al reported that the D locus was cosegregated with the Xtxp97 marker in a sorghum genetic map (Hart et al 2001 ). Both later GWAS and bulked segregant analysis (BSA) have mapped the D locus, and another study narrowed the D locus region with only six genes inside by map-based cloning (Han et al 2015 ; Upadhyaya et al 2022 ; Zhai et al 2014 ). However, the underlying gene and its role in the origin of sweet sorghum remained obscure until two 2018 studies.…”

Genome‑wide identification and characterization of miR396 family members and their target genes GRF in sorghum (Sorghum bicolor (L.) moench)

“…Owing to its excellent adaptability to heat and drought stress, sorghum is a key crop for safeguarding food security in response to climate change [ 4 ]. Recently, sorghum has also been widely used for different purposes, for example, as feed and forage, in brewing, and in biomass energy production, which has a significant effect on global agricultural production [ 5 – 8 ]. In recent years, with the continuous development of animal husbandry and brewery industries, sorghum production has struggled to meet the market demand [ 9 , 10 ].…”