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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #444845

Research Project: Genetic and Phenotypic Characterization of Sugarcane Germplasm

Location: Subtropical Horticulture Research

Project Number: 6038-21000-026-005-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2023
End Date: Aug 31, 2027

The USDA mandate to produce quality food at a lower environmental impact will require developing crop varieties that grow sustainably, are adapted to modern agronomic practices and efficiently use water and nutrient resources. Developing such varieties will require genetically diverse germplasm base that is characterized for agronomically important traits. USDA-ARS-SHRS, Miami, FL maintains the World Collection of Sugarcane and Related Grasses (WCSRG). This collection currently consists of approximately 907 different accessions, a vast majority of which belongs to 10 different Saccharum spp. including 294 S. spontaneum accessions, 134 S. officinarum accessions, 76 S. hybrids accessions, 46 S. robustum accessions, 30 S. sinense accessions, and 21 S. barberi accessions. These accessions originated from different geoclimatic regions around the world and likely harbor genes for adaptation to different climatic stresses, pests, and diseases. Given the climate change and the expected loss of landraces and wild relatives of crops, this collection of sugarcanes will serve as a valuable genetic resource for future breeding and genetics projects. This collection is underutilized, partly because it is not well-characterized genetically and phenotypically.

Descriptor’s data in most germplasm collections have focused primarily on aerial traits, whereas below ground rhizospheric traits such as ratooning ability (RA) and root system architecture (RSA) have largely been lacking. Water and nutrient use efficiency, which are inherently dependent on RSA, are increasingly being investigated for a better understanding of the genetics and Gene X Environment interaction of these traits. Characteristics of root system such as depth, volume and branching patterns, play important roles in accessing water and nutrients in soil. To address deficiency in descriptors data related to root traits, a core collection will be evaluated in containers. Particularly, ratooning ability, which is one of the most important traits targeted by sugarcane breeders, will also be evaluated. Ratooning ability as well as RSA will be separately assessed in sandy and muck soils, which are the two major soil types in the sugarcane growing areas in Florida. USDA-ARS, university and public breeding programs focus on developing sugarcane varieties for these soil types. A trans-disciplinary team of researchers at USDA/ARS and the University of Florida (UF) with expertise in genetics, genomics, bioinformatics, and agronomy will conduct complementary research focused on evaluating and genetically characterizing the sugarcane germplasm. For evaluating RA and RSA, experiments will be set up in pots in three replications. Data collection and analyses on RA and RSA will be conducted according to standard published reports. Molecular markers, especially single nucleotide polymorphisms (SNPs), are actively pursued as a valuable tool for conducting GWAS for agronomically important traits in sugarcanes. In this project, 200K SNP array will be used for genotyping the core sugarcane collection. High resolution SNP genotyping together with the multi-year phenotypic data collected in this project will provide important information for conducting GWAS for identifying molecular markers that are associated with RSA and RA. GWAS will be conducted using ridge regression-best linear unbiased prediction (rrBLUP) and genomic best linear unbiased prediction (gBLUP) models as well as other appropriate models if needed. Analyses will be conducted using GWASPoly V2.0 or other packages that can handle SNP data of different ploidy levels will also be used. In addition to GWAS analyses, heritability and population genetics parameters will be determined using published reports. Anticipated products include morphologic, genetic, and genomic characterization of sugarcane and wild relatives and enhanced data management of genomic resources for sugarcane. Evaluation of wild relatives of Saccharum spp. as well as other closely-related genera in WCSRG will lead to identifying parental germplasm for breeding sugarcanes with high yield, high water use efficiency, and abiotic stress tolerance. These investigations are expected to identify sugarcane accessions and molecular markers for potential application of genomic selection in sugarcane breeding programs.