Unraveling the Genetic Basis of Sorghum Plant Color: Insights into Phenotypic Traits and Fungal Resistance

  • SorghumBase Team
  • 10 June 2024

In sorghum, plant color is a key trait determined by the P and Q genes, with different genotypes resulting in purple (P_Q_), red (P_ qq), or tan (pp Q_ and pp qq) coloration. Beyond aesthetics, plant color is linked to various phenotypes and consumer preferences. For instance, white sorghum grains from tan plants are preferred for both human and animal consumption due to lower tannin content, while purple/red plants have higher levels of total phenols. However, tan plants exhibit lower susceptibility to head blight caused by Fusarium moniliforme, a major fungal pathogen of cereals. Flavonoids such as luteolin, found in higher levels in tan plants, act as phytoalexins against pathogens like Colletotrichum sublineolum. The underlying genetics of plant color involve genes like Sobic.006G226800 (Sb06g029550), which encodes a protein with flavanone 4-reductase activity.

In a recent study, researchers from Anhui Science and Technology University, Anhui Province International Joint Research Center of Forage Bio-breeding and University of Louisiana at Lafayette assessed the plant color of the sorghum mini core collection by scoring the leaf sheath and leaf color at maturity as tan, red, or purple across three different testing environments in China. They conducted association mapping using over 6 million SNP markers and identified candidate genes in eight loci that are strongly linked to plant color. Notably, the qPC6 locus on chromosome 6 was found to be distinct from previously identified QTLs, suggesting multiple genes may control plant color. Candidate genes linked to these loci, such as Sobic.006G149700, a senescence regulator, showed tissue-specific expression patterns, indicating their potential roles in plant color determination. Additionally, they identified a candidate gene, Sobic.005G165700, associated with fungal resistance, highlighting the multifaceted nature of plant color development and its interaction with environmental factors like pathogen attack. The authors found a loose correlation between the degree of linkage and tissue/organ expression of the underlying genes possibly related to the plant color phenotype. Furthermore, allele analysis indicated that none of the linked SNPs can differentiate between red and purple accessions whereas all linked SNPs can differentiate tan from red/purple accessions. These findings provide some insights into the genetics underlying sorghum plant color and offer opportunities to test candidate genes for targeted breeding efforts to enhance desired traits.

SorghumBase examples: 

Figure 1: Sobic.006G149700 is a senescence regulator and the candidate gene for association with plant color located in the peak of the qPC6 locus. Although the gene is located outside of the four plant color QTLs on chromosome 6 identified by Mace and Jordan (2010) and Boyles et al (2017), the above view in SorghumBase shows that it overlaps with QTLs for grain color and carotenoid content.
Figure 2: Consistent with a role in pigmentation, Sobic.006G149700 is highly expressed in leaf (13-18 TPM; Zhang et al, 2018), early inflorescence (25 TPM; Davidson et al, 2012), endosperm (13 TPM; Davidson et al, 2012), and stem (13 TPM; Makita et al, 2012).
Figure 3: Genotypes at the three featured SNPs found to be associated with plant color (5:64621753, 5:64224755 and 6:51113980) are available in SorghumBase for ~900 accessions including 400 Sorghum Association Panel (SAP; Lozano et al, 2021) and 499 additional samples (Boatwright et al, 2022). The SNPs are rs5433814782 at chr5:64621753 with alleles G/C, rs5434363911, a GT/- deletion at chr5:64224754-64224756, and rs266452471 at chr6:51113980 with alleles G/C, just upstream of Sobic.006G149700 in qPC6. Shown in the figure are the genotypes at rs5433814782 for two non-tan or pigmented (as per ICRISAT records) SAP lines: PI533800 or IS18696 is homozygous for the minor A allele, while PI276837 or IS12661 is homozygous for the major allele C. A third SAP line, described as tan (PI533758 or IS18684), did not have a genotype at this SNP. Meanwhile, all three SAP lines were found to be homozygous for the reference and major allele of rs5434363911. This exercise presents SorghumBase as a robust resource to easily identify public germplasm (often characterized for common traits such as plant color in this case) with publicly available genotyping data.

Reference:

Wang L, Tu W, Jin P, Liu Y, Du J, Zheng J, Wang YH, Li J. Genome-wide association study of plant color in Sorghum bicolor. Front Plant Sci. 2024 Apr 10;15:1320844. PMID: 38660439. doi: 10.3389/fpls.2024.1320844. Read more