Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Mace, Emma; Tai, Shuaishuai; Gilding, Edward K.; Li, Yanhong; Prentis, Peter J.; Bian, Lianle; Campbell, Bradley C.; Hu, Wushu; Innes, David J.; Han, Xuelian; Cruickshank, Alan; Changming, Dai; Frère, Céline; Zhang, Haikuan; Hunt, Colleen H.; Wang, Xianyuan; Shatte, Tracey; Wang, Miao; Su, Zhe; Li, Jun; Lin, Xiaozhen; Godwin, Ian D.; Jordan, David R.; Wang, Jun

doi:10.1038/ncomms3320

Cited by 408 publications

(498 citation statements)

References 57 publications

Supporting

Mentioning

456

Contrasting

Order By: Relevance

“…We identified novel traits from our mutant library, such as msd and erl mutants, that could also be applied to sorghum improvement (Burow et al, 2014;Xin et al, 2015). We compared the overlap of EMS-induced mutations with natural variations discovered by genotyping-by-sequencing and wholegenome sequencing in a total of 1016 sorghum lines (Mace et al, 2013;Morris et al, 2013). Only 6659 of 264,978 EMS-induced mutations in the corresponding region were present as natural variations (Supplemental Figure 4B).…”

Section: Discussionmentioning

confidence: 99%

“…To determine the novelty of EMS-induced SNPs from natural variations annotated based on published literature (Mace et al, 2013;Morris et al, 2013), it is necessary to ensure that the EMS-induced SNPs and natural variations are at the same locations. Because all natural variations have been analyzed using the v1.4 sorghum genome annotation, the genes from the v1.4 annotation were first aligned to the v2.1 assembly using BLAST (Altschul et al, 1990).…”

Section: Characterization Of Sorghum Ems-induced Snpsmentioning

confidence: 99%

“…Only genes with a 100% match to the same chromosome from the v2.1 genome assembly were used for the SNP comparison. EMS-induced SNPs were compared with two natural variation sets available from the Gramene database (Monaco et al, 2014): The first population consists of 265,000 SNPs from 971 worldwide accessions, assayed by genotyping-by-sequencing (Morris et al, 2013); the second population consists of six million SNPs, assayed by whole-genome sequencing of 45 S. bicolor and two S. propinquum lines (Mace et al, 2013). The coordination of SNPs within the mapped genes was converted from the v1.4 assembly to v2.1 using a script written in house.…”

Section: Characterization Of Sorghum Ems-induced Snpsmentioning

confidence: 99%

See 2 more Smart Citations

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses

et al. 2016

View full text Add to dashboard Cite

Sorghum (Sorghum bicolor) is a versatile C4 crop and a model for research in family Poaceae. High-quality genome sequence is available for the elite inbred line BTx623, but functional validation of genes remains challenging due to the limited genomic and germplasm resources available for comprehensive analysis of induced mutations. In this study, we generated 6400 pedigreed M4 mutant pools from EMS-mutagenized BTx623 seeds through single-seed descent. Whole-genome sequencing of 256 phenotyped mutant lines revealed >1.8 million canonical EMS-induced mutations, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. To demonstrate the utility of the sequenced sorghum mutant resource, we performed reverse genetics to identify eight genes potentially affecting drought tolerance, three of which had allelic mutations and two of which exhibited exact cosegregation with the phenotype of interest. Our results establish that a large-scale resource of sequenced pedigreed mutants provides an efficient platform for functional validation of genes in sorghum, thereby accelerating sorghum breeding. Moreover, findings made in sorghum could be readily translated to other members of the Poaceae via integrated genomics approaches.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Characterization Of Sorghum Ems-induced Snpsmentioning

confidence: 99%

Section: Characterization Of Sorghum Ems-induced Snpsmentioning

confidence: 99%

See 1 more Smart Citation

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses

et al. 2016

View full text Add to dashboard Cite

show abstract

“…It is a versatile crop capable of growing well under contrasting climatic conditions and high elevations up to 40 o latitude in East Africa (Espinoza and Kelly, 2002;Srinivasa Rao et al, 2014). Sorghum is a staple for over 500 million of the world's poorest people, used for food, feed and fodder purposes (Mace et al, 2013). Its alternative uses include production of beer, alcohol, syrup, bakery items, industrial starch, etc.…”

Section: Introductionmentioning

confidence: 99%

Geographical distribution, diversity and gap analysis of East African sorghum collection conserved at the ICRISAT genebank

Upadhyaya¹,

Narsimha²,

Vetriventhan³

et al. 2017

Aust J Crop Sci

View full text Add to dashboard Cite

The aim of the investigation was to assess the geographical distribution, diversity and gaps in sorghum collection from East African countries conserved at the ICRISAT genebank. The collection represents a total of 12,750 accessions including 11,672 landraces, 877 breeding materials, six improved cultivars, and 195 wild accessions. Passport data and FloraMap, a GIS software were used to assess geographical distribution and identify gaps. Range, mean, variance and phenotypic diversity index were estimated using GENSTAT 13.1. to assess the diversity in the collection. Cultivated sorghums classified into races and intermediate races based on spikelet and panicle morphology differed significantly, and races showed more variation than intermediate races for days to 50% flowering in postrainy season, plant height in rainy season, basal tillers per plant, panicle length, seed width and 100 seed weight. A total of 153 districts located in 50 provinces of 10 East African countries were found as the geographical gaps. Probably due to large variation for maturity, timing of collecting mission, and accessibility to the area under sorghum cultivation, both North and South Sudan were found as the major gaps with seven and 50 districts, respectively. The wild sorghum collection from East African countries belongs to S. bicolor, S. halepense, S. lanceolatum, S. macrochaeta, S. purpureosericeum and S. versicolor. Remaining species of genus sorghum were considered as taxonomic gaps. The gaps identified in the present study need to be explored on a priority basis to collect and conserve most diverse sorghum germplasm.

show abstract

“…Genotyping by sequencing (GBS) has been introduced as a tool to discover polymorphic markers while genotyping with high-throughput sequencing approaches with a low cost per data point (Gupta et al, 2008;Poland and Rife, 2012). The recent resequencing of multiple sorghum genotypes revealed the structuring of genotypes based on racial grouping and also identified novel genetic variability which could be useful for genetic improvements activities (Mace et al, 2013). In addition, genome-wide markers generated by GBS have also been used for diversity analysis and understanding the genetic basis of complex traits and adaptation in sorghum (Morris et al, 2013;Wang et al, 2013).…”

Section: Sorghum Genetic Variability In a Global Contextmentioning

confidence: 99%

Genetic differentiation, heterotic performance and grain yield determinate traits of locally adapted sorghum genotypes in contrasting environments in Ethiopia

Mindaye¹

View full text Add to dashboard Cite

The increase superiority in characteristics such as size, growth rate, fertility, yield and general fitness of hybrids produced by crossing genetically diverse inbred parents is well established in many plant and animal species. This phenomenon has been exploited to produce commercial cultivars in a range of crop species including sorghum.In sorghum F1 hybrid seed is produced by crossing genetically distinct restorer (R lines) and cytoplasmic male sterile seed parent (A lines). In the developed world commercial cultivars are almost exclusively F1 hybrids and are increasingly being used in the developing countries. In spite of the yield advantage in some circumstances, however, hybrids developed using introduced parental lines have not been adopted by Ethiopian farmers primarily because of the extra cost of purchasing seed has not been outweighed by the benefits of introduced hybrids in particular the lack of farmer preferred traits such as tall stature and larger grain size. The development of hybrids using locally adapted genotypes could have the potential to overcome the shortcomings of introduced hybrids. However, the complex cytoplasmic male sterility system and prevalence of restorer genes complicate the development of new Additionally, the hybrids derived from these locally adapted genotypes will have the benefit of containing farmers preferred traits. The groups most divergent from the introduced A/B lines were the Ethiopian landraces adapted to highland and intermediate agro-ecologies and a subset of lowland adapted genotypes. These genotype groups were also grouped distinctly from the introduced R lines, and hence provide highly divergent parental lines for hybrid development in Ethiopia.The performance and magnitude of heterosis of 139 F1 hybrids, derived from introduced seed parents crossed with selected locally adapted genotypes and introduced R lines, were evaluated in three contrasting environments. The lowland adapted hybrids displayed a mean better parent heterosis (BPH)iii of 19% and a 29% increase in grain yield, on average, in comparison to the hybrids derived from the introduced R lines. In addition, these hybrids were also found to be superior in plant height and grain weight. The mean BPH for grain yield for the highland adapted hybrids was 16% in the highland and 52 % in the intermediate, in addition to increased grain weight. The magnitude of heterosis between the three hybrid groups reflected the genetic distance between the genotype groups with the A/B lines.These results highlight the potential of locally adapted genotypes for the exploitation of heterosis in Ethiopia.In order to understand the genetic basis of increased hybrid performance, the relationship between yield component traits was assessed and the genetic variance for each subset of hybrid group was partitioned into parental lines and their interaction effects. In the lowland environment, increase in grain number and grain weight contributed to increased yield of the lowland adapted hybrids in comparison to the intro...

show abstract

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Cited by 408 publications

References 57 publications

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses

Geographical distribution, diversity and gap analysis of East African sorghum collection conserved at the ICRISAT genebank

Genetic differentiation, heterotic performance and grain yield determinate traits of locally adapted sorghum genotypes in contrasting environments in Ethiopia

Contact Info

Product

Resources

About