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Title: Discovering the desirable alleles contributing to the lignocellulosic biomass traits in Saccharum germplasm collections for energy cane improvement

Abstract

1) The success in crop improvement programs depends largely on the extent of genetic variability available. Germplasm collections assembles all the available genetic resources and are critical for long-term crop improvement. This world sugarcane germplasm collection contains enormous genetic variability for various morphological traits, biomass yield components, adaptation and many quality traits, prospectively imbeds a large number of valuable alleles for biofuel traits such as high biomass yield, quantity and quality of lignocelluloses, stress tolerance, and nutrient use efficiency. The germplasm collection is of little value unless it is characterized and utilized for crop improvement. In this project, we phenotypically and genotypically characterized the sugarcane world germplasm collection (The results were published in two papers already and another two papers are to be published). This data will be made available for public to refer to for germplasm unitization specifically in the sugarcane and energy cane breeding programs. In addition, we are identifying the alleles contributing to the biomass traits in sugarcane germplasm. This part of project is very challenging due to the large genome and highly polyploid level of this crop. We firstly established a high throughput sugarcane genotyping pipeline in the genome and bioinformatics era (a paper is publishedmore » in 2016). We identified and modified a software for genome-wide association analysis of polyploid species. The results of the alleles associated to the biomass traits will be published soon, which will help the scientific community understand the genetic makeup of the biomass components of sugarcane. Molecular breeders can develop markers for marker assisted selection of biomass traits improvement. Further, the development and release of new energy cane cultivars through this project not only improved genetic diversity but also improved dry biomass yields and resistance to diseases. These new cultivars were tested on marginal soils in Florida and showed very promising yield potential that is important for the successful use of energy cane as a dedicated feedstock for lignocellulosic ethanol production. 2) Multiple techniques at different project progress stages were utilized. For example, for the whole world germplasm accession genotyping, a cheap widely used SSR marker genotyping platform was utilized due to the large number of samples (over thousand). But the throughput of this technique is low in generating data points. However, the purpose the genotyping is to form a core collection for further high throughput genotyping. Thus the results from the SSR genotyping was quite good enough to generated the core collection. To genotype the few hundred core collection accessions, an target enrichment sequencing technology was used, which is not only high throughput in generating large number of genotyping data, but also has the candidate genes targeted to genotyping. The data generated would be sufficient in identifying the alleles contributing to the traits of interests. All the techniques used in this project are effective though extensive time was invested specifically for establish the pipeline in the experimental design, data analysis, and different approach comparison. 3) the research can benefit to the public in polyploid genotyping and new and cost efficient genotyping platform development« less

Authors:
 [1];  [1]
  1. Univ. of Florida, Gainesville, FL (United States)
Publication Date:
Research Org.:
Univ. of Florida, Gainesville, FL (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
Contributing Org.:
BP company, Biofuels; USDA ARS Subtropical; Horticulture Research Station
OSTI Identifier:
1347688
Report Number(s):
DOE-UF-6995
DOE Contract Number:  
SC0006995
Resource Type:
Technical Report
Resource Relation:
Related Information: None
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; sugarcane; energy cane; genome; biomass; allele

Citation Formats

Wang, Jianping, and Sandhu, Hardev. Discovering the desirable alleles contributing to the lignocellulosic biomass traits in Saccharum germplasm collections for energy cane improvement. United States: N. p., 2017. Web. doi:10.2172/1347688.
Wang, Jianping, & Sandhu, Hardev. Discovering the desirable alleles contributing to the lignocellulosic biomass traits in Saccharum germplasm collections for energy cane improvement. United States. https://doi.org/10.2172/1347688
Wang, Jianping, and Sandhu, Hardev. 2017. "Discovering the desirable alleles contributing to the lignocellulosic biomass traits in Saccharum germplasm collections for energy cane improvement". United States. https://doi.org/10.2172/1347688. https://www.osti.gov/servlets/purl/1347688.
@article{osti_1347688,
title = {Discovering the desirable alleles contributing to the lignocellulosic biomass traits in Saccharum germplasm collections for energy cane improvement},
author = {Wang, Jianping and Sandhu, Hardev},
abstractNote = {1) The success in crop improvement programs depends largely on the extent of genetic variability available. Germplasm collections assembles all the available genetic resources and are critical for long-term crop improvement. This world sugarcane germplasm collection contains enormous genetic variability for various morphological traits, biomass yield components, adaptation and many quality traits, prospectively imbeds a large number of valuable alleles for biofuel traits such as high biomass yield, quantity and quality of lignocelluloses, stress tolerance, and nutrient use efficiency. The germplasm collection is of little value unless it is characterized and utilized for crop improvement. In this project, we phenotypically and genotypically characterized the sugarcane world germplasm collection (The results were published in two papers already and another two papers are to be published). This data will be made available for public to refer to for germplasm unitization specifically in the sugarcane and energy cane breeding programs. In addition, we are identifying the alleles contributing to the biomass traits in sugarcane germplasm. This part of project is very challenging due to the large genome and highly polyploid level of this crop. We firstly established a high throughput sugarcane genotyping pipeline in the genome and bioinformatics era (a paper is published in 2016). We identified and modified a software for genome-wide association analysis of polyploid species. The results of the alleles associated to the biomass traits will be published soon, which will help the scientific community understand the genetic makeup of the biomass components of sugarcane. Molecular breeders can develop markers for marker assisted selection of biomass traits improvement. Further, the development and release of new energy cane cultivars through this project not only improved genetic diversity but also improved dry biomass yields and resistance to diseases. These new cultivars were tested on marginal soils in Florida and showed very promising yield potential that is important for the successful use of energy cane as a dedicated feedstock for lignocellulosic ethanol production. 2) Multiple techniques at different project progress stages were utilized. For example, for the whole world germplasm accession genotyping, a cheap widely used SSR marker genotyping platform was utilized due to the large number of samples (over thousand). But the throughput of this technique is low in generating data points. However, the purpose the genotyping is to form a core collection for further high throughput genotyping. Thus the results from the SSR genotyping was quite good enough to generated the core collection. To genotype the few hundred core collection accessions, an target enrichment sequencing technology was used, which is not only high throughput in generating large number of genotyping data, but also has the candidate genes targeted to genotyping. The data generated would be sufficient in identifying the alleles contributing to the traits of interests. All the techniques used in this project are effective though extensive time was invested specifically for establish the pipeline in the experimental design, data analysis, and different approach comparison. 3) the research can benefit to the public in polyploid genotyping and new and cost efficient genotyping platform development},
doi = {10.2172/1347688},
url = {https://www.osti.gov/biblio/1347688}, journal = {},
number = ,
volume = ,
place = {United States},
year = {2017},
month = {3}
}