Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum

Nida, Habte; Girma, Gezahegn; Mekonen, Moges; Tirfessa, Alemu; Seyoum, Amare; Bejiga, Tamirat; Birhanu, Chemeda; Dessalegn, Kebede; Senbetay, Tsegau; Ayana, Getachew; Tesso, Tesfaye; Ejeta, Gebisa; Mengiste, Tesfaye

doi:10.1007/s00122-020-03762-2

Cited by 28 publications

(23 citation statements)

References 84 publications

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“…The grain mold resistance of the genotype is significantly improved by a darker glume color, higher content of phenols, and the hardness of the seed (Audilakshmi et al 1999 ). Recently, a known SNP (S4_62316425) in the TAN1 gene, a regulator of tannin accumulation in sorghum grain, was detected with a significant association with grain mold resistance (Nida et al 2021 ), as the processing of phenolic acids improves the digestibility of tannins in sorghum. The processing of grain sorghum in dry heat (95 °C for 20 min and 121 °C for 30 min) can depolymerize the condensed tannins in sorghum (Barros et al 2012 ), which can increase their bioavailability.…”

Section: Sorghum Polyphenolsmentioning

confidence: 99%

RETRACTED ARTICLE: Sorghum polyphenols: plant stress, human health benefits, and industrial applications

Kumari

Kumar

et al. 2021

Planta

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Main conclusion Various phenolic compounds of sorghum are effective in the management of abiotic stress (salt, nutrients) and biotic stress (caused by birds, fungi and aphids). The health and industrial application of phenolics is mainly contributed by inherent antioxidant and nutraceutical potential. Abstract In a natural environment, plant growth is affected by various biotic and abiotic stresses. In every ecosystem, the presence of a wide range of harmful biological agents (bacteria, fungi, nematodes, mites, and insects) and undesirable environmental factors (drought, salinity, heat, excessive or low rainfall, etc.) may cause a heavy loss in crop productivity. Being sessile during evolution, plants have evolved multiple defense mechanisms against various types of microbial pathogens and environmental stresses. A plant’s natural defense system produces some compounds named secondary metabolites, which include phenolics, terpenes, and nitrogen. The phenolic profile of grain sorghum, the least utilized staple crop, is unique, more diverse, and more abundant than in any other common cereal grain. It mainly contains phenolic acids, 3-deoxyanthocyanidins and condensed tannins. Sorghum polyphenols play a major role in plant defense against biotic and abiotic stresses and have many additional health benefits along with various industrial applications. The objective of this review is to discuss the phenolic compounds derived from grain sorghum and describe their role in plant defense, human health, and industrial applications.

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Section: Sorghum Polyphenolsmentioning

confidence: 99%

RETRACTED ARTICLE: Sorghum polyphenols: plant stress, human health benefits, and industrial applications

Kumari

Kumar

et al. 2021

Planta

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“…Most SNPs were only found in one method. Therefore, it may be prudent to use multiple methods to conduct a GWAS survey (Nida et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress

Shi

et al. 2022

Front. Plant Sci.

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Sunflower is one of the most important oil crops in the world, and drought stress can severely limit its production and quality. To understand the underlying mechanism of drought tolerance, and identify candidate genes for drought tolerance breeding, we conducted a combined genome-wide association studies (GWAS) and RNA-seq analysis. A total of 226 sunflower inbred lines were collected from different regions of China and other countries. Eight phenotypic traits were evaluated under control and drought stress conditions. Genotyping was performed using a Specific-Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 934.08 M paired-end reads were generated, with an average Q30 of 91.97%. Based on the 243,291 polymorphic SLAF tags, a total of 94,162 high-quality SNPs were identified. Subsequent analysis of linkage disequilibrium (LD) and population structure in the 226 accessions was carried out based on the 94,162 high-quality SNPs. The average LD decay across the genome was 20 kb. Admixture analysis indicated that the entire population most likely originated from 11 ancestors. GWAS was performed using three methods (MLM, FarmCPU, and BLINK) simultaneously. A total of 80 SNPs showed significant associations with the 8 traits (p < 1.062 × 10−6). Next, a total of 118 candidate genes were found. To obtain more reliable candidate genes, RNA-seq analysis was subsequently performed. An inbred line with the highest drought tolerance was selected according to phenotypic traits. RNA was extracted from leaves at 0, 7, and 14 days of drought treatment. A total of 18,922 differentially expressed genes were obtained. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed up-regulated genes were mainly enriched in the branched-chain amino acid catabolic process, while the down-regulated genes were mainly enriched in the photosynthesis-related process. Six DEGs were randomly selected from all DEGs for validation; these genes showed similar patterns in RNA-seq and RT-qPCR analysis, with a correlation coefficient of 0.8167. Through the integration of the genome-wide association study and the RNA-sequencing, 14 candidate genes were identified. Four of them (LOC110885273, LOC110872899, LOC110891369, LOC110920644) were abscisic acid related protein kinases and transcription factors. These genes may play an important role in sunflower drought response and will be used for further study. Our findings provide new insights into the response mechanisms of sunflowers against drought stress and contribute to further genetic breeding.

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“…Another recent SGM association study employing 635 Ethiopian genotypes by Nida et al (2021) identified a collection of protein-coding loci, and consistently detected SNPs within the TAN1 coding region. The authors suggested TAN1's role in the flavonoid pathway affecting biosynthesis of 3-DAs and tannins could contribute to TAN1's role in grain mold resistance.…”

Section: Enzymatic Conversion Of Naringenin By F3h -The Synthesis and Properties Of Condensed Tannins (Proanthocyanidins)mentioning

confidence: 92%

“…Condensed tannins (proanthocyanidins) are well understood for their roles in increased antioxidant capabilities and significant correlations with SGM resistance (Harris and Burns, 1973;Forbes, 1986;Melake-Berhan et al, 1996;Dicko et al, 2005;Cuevas et al, 2019b). The presence of condensed tannins throughout SGM resistant germplasm is interesting, as there is little knowledge to suggest condensed tannins demonstrate direct toxicity to fungal pathogens as do products of other branches of the flavonoid biosynthesis pathway such as 3-DAs and flavones (Melake-Berhan et al, 1996;Du et al, 2009;Nida et al, 2021). Regardless, the use of condensed tannins is limited in sorghum germplasms for their reduction in protein digestibility of animals.…”

Section: Enzymatic Conversion Of Naringenin By F3h -The Synthesis and Properties Of Condensed Tannins (Proanthocyanidins)mentioning

confidence: 99%

The Sorghum Grain Mold Disease Complex: Pathogens, Host Responses, and the Bioactive Metabolites at Play

2021

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Grain mold is a major concern in sorghum [Sorghum bicolor (L.) Moench] production systems, threatening grain quality, safety, and nutritional value as both human food and livestock feed. The crop’s nutritional value, environmental resilience, and economic promise poise sorghum for increased acreage, especially in light of the growing pressures of climate change on global food systems. In order to fully take advantage of this potential, sorghum improvement efforts and production systems must be proactive in managing the sorghum grain mold disease complex, which not only jeopardizes agricultural productivity and profitability, but is also the culprit of harmful mycotoxins that warrant substantial public health concern. The robust scholarly literature from the 1980s to the early 2000s yielded valuable insights and key comprehensive reviews of the grain mold disease complex. Nevertheless, there remains a substantial gap in understanding the complex multi-organismal dynamics that underpin the plant-pathogen interactions involved – a gap that must be filled in order to deliver improved germplasm that is not only capable of withstanding the pressures of climate change, but also wields robust resistance to disease and mycotoxin accumulation. The present review seeks to provide an updated perspective of the sorghum grain mold disease complex, bolstered by recent advances in the understanding of the genetic and the biochemical interactions among the fungal pathogens, their corresponding mycotoxins, and the sorghum host. Critical components of the sorghum grain mold disease complex are summarized in narrative format to consolidate a collection of important concepts: (1) the current state of sorghum grain mold in research and production systems; (2) overview of the individual pathogens that contribute to the grain mold complex; (3) the mycotoxin-producing potential of these pathogens on sorghum and other substrates; and (4) a systems biology approach to the understanding of host responses.

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Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum

Cited by 28 publications

References 84 publications

RETRACTED ARTICLE: Sorghum polyphenols: plant stress, human health benefits, and industrial applications

RETRACTED ARTICLE: Sorghum polyphenols: plant stress, human health benefits, and industrial applications

Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress

The Sorghum Grain Mold Disease Complex: Pathogens, Host Responses, and the Bioactive Metabolites at Play

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