Whole-genome resequencing of Sorghum bicolor and S. bicolor × S. halepense lines provides new insights for improving plant agroecological characteristics

Abstract

Sorghum (Sorghum bicolor L. (Moench)) is the world’s fifth economically most important cereal and is a staple particularly in the semi-arid tropics of Africa and Asia. Genetic gains in this crop can benefit from wild relatives such as Sorghum halepense. Genome sequences including those from this wild species can boost the study of genome-wide and intraspecific variation for dissecting the genetic basis and improving important traits in sorghum. The whole-genome resequencing carried out in this work on a panel of 172 populations of S. bicolor and S. bicolor × S. halepense (SbxSh) advanced lines generated a total of 567,046,841 SNPs, 91,825,474 indels, 1,532,171 SVs, and 4,973,961 CNVs. Clearly, SbxSh accumulated more variants and mutations with powerful effects on genetic differentiation. A total of 5,548 genes private to SbxSh mapped to biological process GO enrichment terms; 34 of these genes mapped to root system development (GO: 0022622). Two of the root specific genes i.e., ROOT PRIMORDIUM DEFECTIVE 1 (RPD1; GeneID: 8054879) and RETARDED ROOT GROWTH (RRG, GeneID: 8072111), were found to exert direct effect on root growth and development. This is the first report on whole-genome resequencing of a sorghum panel that includes S. halepense genome. Mining the private variants and genes of this wild species can provide insights capable of boosting sorghum genetic improvement, particularly the perenniality trait that is compliant with agroecological practices, sustainable agriculture, and climate change resilience.

Discarded sequencing reads uncover natural variation in pest resistance inThlaspi arvense

“…With the decreasing cost of sequencing and increasing large-scale and single-species sequencing projects e.g. (37)(38)(39)(40)(41)(42)(43), the number of datasets suitable for such analyses is set to rapidly increase in the near future.…”

“…The goals of our study were thus two-fold: i) to contribute to a mechanistic understanding of pest resistance in Thlaspi arvense, and, more generally, ii) to explore whether non-target reads from plant sequencing can be used as proxies for studying plant biotic interactions. Considering that we are moving towards an increasingly sequencing-prone world, where more and larger datasets are being generated for many species (37)(38)(39)(40)(41)(42)(43), the use of non-target reads will likely have very broad potential.…”

Unveiling shared genetic regulators for plant architectural and biomass yield traits in sorghum

“…The dry mass fraction of plant parts, such as stems, leaves, tillers, and panicles, is commonly called biomass and production of lignocellulosic biofuel increases with increasing biomass (Habyarimana et al ., 2020; Habyarimana et al ., 2022). Of this, stems and leaves account for 80-85% of harvested biomass from sorghum plants (Mullet et al ., 2014).…”

Investigation on Physicochemical Properties and Anti-nutritional content of the three sorghum Varieties Grown in Ethiopia

“…It is a versatile ingredient in African and Asian diets and is a staple food for around 500 million people in 30 countries across Africa and Asia (Khoddami et al, 2023). In Ethiopia, it is the primary source of stable food, ranking second in overall production and third in terms of production per hectare and cultivated land area (Habyarimana et al, 2022). From 2000/01 to 2020/21, Ethiopia produced an average total of 69,979,742 tons of sorghum (Bezabih et al, 2023).…”