Extensive variation within the pan-genome of cultivated and wild sorghum

Tao, Yongfu; Luo, Hong; Xu, Jiabao; Cruickshank, Alan; Zhao, Xianrong; Teng, Fei; Hathorn, Adrian; Wu, Xiaoyuan; Liu, Yuanming; Shatte, Tracey; Jordan, David R.; Jing, Hai‐Chun; Mace, Emma

doi:10.1038/s41477-021-00925-x

Cited by 119 publications

(103 citation statements)

References 63 publications

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“…Compared with high-quality genome sequencing from individual lines, pan-genome sequences, which consist of genome sequences assembled de novo from many representative genetic diverse lines, can capture the full genomic diversity of a species. Tao et al (2021) performed a de novo assembly of 13 diverse lines representing the cultivated sorghum and its wild relatives. Along with the publicly available genome sequences, 16 genome sequences were used to construct the sorghum pan-genome sequence.…”

Section: Genome Sequencesmentioning

confidence: 99%

“…Despite its value, sorghum breeding and genomic studies have lagged other crops like rice and maize. With the completion of a sorghum reference genome sequenced over a decade ago (Paterson et al 2009), the construction of several sorghum association panels (SAP) (Casa et al 2008;Morris et al 2013b;Upadhyaya et al 2009), the establishment of mutant libraries, the recent completion of sorghum pangenomes, the availability of sorghum gene expression atlas and the development of sorghumbase online (Addo-Quaye et al 2018;Jiao et al 2016;Xin et al 2008;Tao et al 2021;Makita et al 2015;Shakoor et al 2014), sorghum research has entered an exciting new age. With the vast resources available to producers and researchers, sorghum will become a critical crop for addressing global food and energy security in a changing global climate.…”

Section: Introductionmentioning

confidence: 99%

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Sorghum genetic, genomic, and breeding resources

Xin

Wang²,

Cuevas

et al. 2021

Planta

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Main conclusion Sorghum research has entered an exciting and fruitful era due to the genetic, genomic, and breeding resources that are now available to researchers and plant breeders. Abstract As the world faces the challenges of a rising population and a changing global climate, new agricultural solutions will need to be developed to address the food and fiber needs of the future. To that end, sorghum will be an invaluable crop species as it is a stress-resistant C4 plant that is well adapted for semi-arid and arid regions. Sorghum has already remained as a staple food crop in many parts of Africa and Asia and is critically important for animal feed and niche culinary applications in other regions, such as the United States. In addition, sorghum has begun to be developed into a promising feedstock for forage and bioenergy production. Due to this increasing demand for sorghum and its potential to address these needs, the continuous development of powerful community resources is required. These resources include vast collections of sorghum germplasm, high-quality reference genome sequences, sorghum association panels for genome-wide association studies of traits involved in food and bioenergy production, mutant populations for rapid discovery of causative genes for phenotypes relevant to sorghum improvement, gene expression atlas, and online databases that integrate all resources and provide the sorghum community with tools that can be used in breeding and genomic studies. Used in tandem, these valuable resources will ensure that the rate, quality, and collaborative potential of ongoing sorghum improvement efforts is able to rival that of other major crops.

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Section: Genome Sequencesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sorghum genetic, genomic, and breeding resources

Xin

Wang²,

Cuevas

et al. 2021

Planta

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“…Given the ubiquity of GxExM interactions for crop grain yield within an agricultural TPE, it is expected that further developments in the domain of enviromics will continue and their applications will expand as plant breeders incorporate these technologies within their breeding operations. With the continuing advances in crop genomics (Morrell et al, 2012;Yuan et al, 2017;Tao et al, 2021;Varshney et al, 2021) and phenotyping (Araus and Cairns, 2014;Araus et al, 2018;Van Eeuwijk et al, 2019;Smith et al, 2021), a wide array of suitable genomic predictors are available and becoming cost-effective options for many crop breeding applications. Agronomists and physiologists have invested in the development of methods for measuring important environmental variables (Chenu et al, 2011;Guan et al, 2017;Smith et al, 2021) and suitable crop models to integrate the multiple influences of environmental conditions on yield outcomes for different genotypes (Chapman et al, 2003;Messina et al, 2006Messina et al, , 2018Messina et al, , 2019Chenu et al, 2009;Holzworth et al, 2014;Muller and Martre, 2019;Wang et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Can We Harness “Enviromics” to Accelerate Crop Improvement by Integrating Breeding and Agronomy?

Cooper¹,

Messina²

2021

Front. Plant Sci.

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The diverse consequences of genotype-by-environment (GxE) interactions determine trait phenotypes across levels of biological organization for crops, challenging our ambition to predict trait phenotypes from genomic information alone. GxE interactions have many implications for optimizing both genetic gain through plant breeding and crop productivity through on-farm agronomic management. Advances in genomics technologies have provided many suitable predictors for the genotype dimension of GxE interactions. Emerging advances in high-throughput proximal and remote sensor technologies have stimulated the development of “enviromics” as a community of practice, which has the potential to provide suitable predictors for the environment dimension of GxE interactions. Recently, several bespoke examples have emerged demonstrating the nascent potential for enhancing the prediction of yield and other complex trait phenotypes of crop plants through including effects of GxE interactions within prediction models. These encouraging results motivate the development of new prediction methods to accelerate crop improvement. If we can automate methods to identify and harness suitable sets of coordinated genotypic and environmental predictors, this will open new opportunities to upscale and operationalize prediction of the consequences of GxE interactions. This would provide a foundation for accelerating crop improvement through integrating the contributions of both breeding and agronomy. Here we draw on our experience from improvement of maize productivity for the range of water-driven environments across the US corn-belt. We provide perspectives from the maize case study to prioritize promising opportunities to further develop and automate “enviromics” methodologies to accelerate crop improvement through integrated breeding and agronomic approaches for a wider range of crops and environmental targets.

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“…We compared the sequence of S. bicolor reference genome v3.1.1 and the sequence based on the alternate allele discovered at the SNP position Sb10-5394955 with the recently published sorghum pangenome data (Tao et al, 2021). The gene sequence was selected from the reference genome (v3.1.1) and blasted (blastn: 2.2.31; Camacho and Madden, 2013) against the individual thirteen assembled genomes from the sorghum pangenome dataset.…”

Section: Association Mapping and Candidate Gene Identificationmentioning

confidence: 99%

Genetic Architecture of Novel Sources for Reproductive Cold Tolerance in Sorghum

et al. 2021

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Enhancements in reproductive cold tolerance of sorghum are essential to expand growing areas into both high-latitude temperate areas and tropical high-altitude environments. Here we present first insights into the genetic architecture of this trait via genome-wide association studies in a broad genetic diversity set (n = 330) phenotyped in multi-location field trials including high-altitude tropical (Mexico) and high-latitude temperate (Germany) environments. We observed a high degree of phenotypic variation and identified several novel, temperate-adapted accessions with superior and environmentally stable cold tolerance. Good heritability indicates strong potential for implementation of reproductive cold tolerance in breeding. Although the trait was found to be strongly quantitative, promising genomic regions with multiple-trait associations were found, including hotspots on chromosomes 3 and 10 which contain candidate genes implicated in different developmental and survival processes under abiotic stress conditions.

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Extensive variation within the pan-genome of cultivated and wild sorghum

Cited by 119 publications

References 63 publications

Sorghum genetic, genomic, and breeding resources

Sorghum genetic, genomic, and breeding resources

Can We Harness “Enviromics” to Accelerate Crop Improvement by Integrating Breeding and Agronomy?

Genetic Architecture of Novel Sources for Reproductive Cold Tolerance in Sorghum

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