Fiber composition of a diversity panel of the world collection of sugarcane (Saccharum spp.) and related grasses

Todd, James; Sandhu, Hardey; Binder, Joe; Arundale, Rebecca A.; Gordon, Vanessa S.; Jiang, Song; Glaz, B.; Wang, Jianping

doi:10.1590/1678-4499.2016525

Cited by 9 publications

(6 citation statements)

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“…During August 2014, nine yield components were measured for the sugarcane diversity with three replicates on ratoon plants including stalk diameter, leaf width, leaf length, stalk number, internode length, brix, total weight, dry weight and water content (Todd et al 2017). In brief, brix, stalk number, stalk diameter, internode length, leaf width, and leaf length of the leaf at the top visible dewlap were recorded for each plant before harvesting.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Yang

Luo

Todd

et al. 2018

Preprint

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25Sugarcane (Saccharum spp.) is an important economic crop, contributes up to 80% of 26 sugar and approximately 60% bio-fuel globally. To meet the increased demand for sugar and 27 bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield 28 components. Therefore, dissection of causal DNA sequence variants is of great importance by 29 providing genetic resources and fundamental information for crop improvement. In this study, 30 we evaluated and analyzed nine yield components in a sugarcane diversity panel consisting of 31 308 accessions primarily selected from the "world collection of sugarcane and related grasses". 32 By genotyping the diversity panel using target enrichment sequencing, we identified a large 33 number of sequence variants. Genome-wide association study between the markers and traits 34 were conducted with dosages and gene actions taken into consideration. In total, 217 non-35 redundant markers and 225 candidate genes were identified to be significantly associated with 36 the yield components, which can serve as a comprehensive genetic resource database for future 37 gene identification, characterization, and selection for sugarcane improvement. We further 38 investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 39 ROHs, and found that the occurrence of ROH in the genome were non-random and probably 40 under selection. ROHs were associated with total weight and dry weight, and high ROHs 41 resulted in decrease of the two traits. This study approved that genomic inbreeding has led to 42 negative impacts on sugarcane yield. 43 GWAS 45 46As an important cash crop, sugarcane (Saccharum spp.) contributes up to 80% of sugar 48 and approximately 60% bio-fuel globally (Dahlquist 2013). To meet the increasing global 49 demand for sugar and bio-fuel, sugarcane harvest area in the world has increased from 22.7 to 50 26.8 million hectares in the last ten years (FAO 2016). However, cropping areas for sugarcane 51 could not be increased indefinitely due to the limited farming land areas and competition with 52 food crops. In order to sustainably improve sugarcane production, breeding sugarcane cultivars 53 with high performance for yield components is critical. Thus, evaluating yield components in 54 sugarcane germplasm and dissecting the genetic basis of causal sequence variants are of great 55 importance to fulfill this strategy by providing tools and genetic resources. 56 The Saccharum genus consists of two wild species (S. spontaneum and S. robustum) 57 and four cultivated species (S. officinarum, S. barberi, S. sinence, and S. edule) (Daniels and 58 Roach 1987). All the Saccharum species are readily intercrossed except sterile S. edule. Modern 59 sugarcane hybrids were primarily derived from inter-species hybridization between S. 60 spontaneum (2n = 40-128, x = 8) and S. officinarum (2n = 80, x = 10) followed by several 61 backcrosses with S. officinarum. Therefore, modern sugarcane hybrids have a chromoso...

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Section: Methodsmentioning

confidence: 99%

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Yang

Luo

Todd

et al. 2018

Preprint

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“…In August 2014, nine yield traits were measured within the sugarcane diversity panel on ratoon plants, with three replicates. The evaluated traits includes stalk diameter, leaf width, leaf length, stalk number, internode length, Brix, total weight, dry weight, and water content (Todd et al, 2017). In brief, the Brix, stalk number, stalk diameter, internode length, leaf width, and leaf length of the leaf at the top visible dewlap were recorded for each plant before harvesting.…”

Section: Phenotyping and Data Treatmentmentioning

confidence: 99%

“…Nine yield traits, including Brix, stalk number, stalk diameter, internode length, and width and length of the leaf at the top visible dewlap had previously been recorded for the diversity panel of 308 lines including 299 germplasm accessions and nine sugarcane clones (Todd et al, 2017). All the traits in this panel were normally distributed, except for stalk number (Supplemental Figure S1), which was transformed further.…”

Section: Correlation and Path Coefficient Analysis Of Yield Traitsmentioning

confidence: 99%

“…Previously, a diversity panel of 299 accessions selected from the WCSRG on the basis of phenotypic and genotypic data, plus nine sugarcane cultivars and breeding materials (Nayak et al, 2014;Todd et al, 2014) were deeply sequenced in their gene coding regions (Yang et al, 2019) and multiple yield related traits were evaluated with three replicates (Todd, Sandhu, Hale, Glaz, & Wang, 2017). In this study, we leveraged the phenotypic data collected earlier and the large amounts of sequence variants with a confident dosage resolution in this diversity panel called from the deep sequencing data, and performed GWAS with the GWASpoly software in sugarcane.…”

Section: Introductionmentioning

confidence: 99%

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Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)

et al. 2020

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Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome-wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield. Abbreviations: DAPC, discriminant analysis of principal components; GWAS, genome-wide association study; indels, insertions and deletions; NGS, next-generation sequencing; NROH, total number of ROHs; ROH, run of homozygosity; SROH, sum total length of ROHs; SNP, single nucleotide polymorphisms; TES, target enrichment sequencing; WCSRG, world collection of sugarcane and related grasses. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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“…On the other hand, the WCSRG was phenotypically characterized by eight traits and a similar core collection was developed based on morphological traits ( Todd et al, 2014 ). A diversity panel representing the WCSRG were selected by weighing in different parameters from combination of both phenotypic and genotypic data, which, not only serves as an association population to discover the desirable alleles in the future, but also can be utilized in the breeding program for crop improvement as they have been thoroughly evaluated for various traits ( Todd et al, 2017 ).…”

Section: Genetic Resources For Sugarcane Biomass Improvementmentioning

confidence: 99%

Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement

et al. 2018

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Lignocellulosic biomass has become an emerging feedstock for second-generation bioethanol production. Sugarcane (Saccharum spp. hybrids), a very efficient perennial C4 plant with a high polyploid level and complex genome, is considered a top-notch candidate for biomass production due to its salient features viz. fast growth rate and abilities for high tillering, ratooning, and photosynthesis. Energy cane, an ideal type of sugarcane, has been bred specifically as a biomass crop. In this review, we described (1) biomass potentials of sugarcane and its underlying genetics, (2) challenges associated with biomass improvement such as large and complex genome, narrow gene pool in existing commercial cultivars, long breeding cycle, and non-synchronous flowering, (3) available genetic resources such as germplasm resources, and genomic and cell wall-related databases that facilitate biomass improvement, and (4) mining candidate genes controlling biomass in genomic databases. We extensively reviewed databases for biomass-related genes and their usefulness in biofuel generation. This review provides valuable resources for sugarcane breeders, geneticists, and broad scientific communities involved in bioenergy production.

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Fiber composition of a diversity panel of the world collection of sugarcane (Saccharum spp.) and related grasses

Cited by 9 publications

References 36 publications

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)

Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement

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