Development and Integration of an SSR-Based Molecular Identity Database into Sugarcane Breeding Program

Abstract

Abstract:Sugarcane breeding is very difficult and it takes 12 to 14 years to develop a new cultivar for commercial production. This is because sugarcane varieties are highly polyploid, inter-specific hybrids with 100 to 130 chromosomes that may vary across geographical areas. Other obstacles/constraints include the small size of flowers that may not synchronize but may self-pollinate, difficulty in distinguishing hybrids from self progenies, extreme (GˆE) interactive effect, and potential variety mis-identification during vegetative propagation and varietal exchange. To help cane breeders circumvent these constraints, a simple sequence repeats (SSR)-based molecular identity database has been developed at the United States Department of Agriculture-Agricultural Research Service, Sugarcane Research Unit in Houma, LA. Since 2005, approximately 2000 molecular identities have been constructed for clones of sugarcane and related Saccharum species that cover geographical areas including Argentina, Australia, Bangladesh, China, Colombia, India, Mexico, Pakistan, South Africa, Thailand, USA (Louisiana, Florida, Texas, and Hawaii), and Venezuela. The molecular identity database is updated annually and has been utilized to: (1) provide molecular descriptors to newly registered cultivars; (2) identify in a timely fashion any mislabeled or unidentifiable clones from cross parents and field evaluation plots; (3) develop de novo clones of energy cane with S. spontaneum cytoplasm; (4) provide clone-specific fingerprint information for assessing cross quality and paternity of polycross; (5) determine genetic relatedness of parental clones; (6) select F 1 hybrids from (eliteˆwild) or (wildˆelite) crosses; and (7) investigate the inheritance of SSR markers in sugarcane. The integration of the molecular identity database into the sugarcane breeding program may improve the overall efficacy of cultivar development and commercialization.Keywords: sugarcane breeding; SSR; molecular identity database Generally speaking, there are probably nine key issues that affect both the productivity and the sustainability of sugarcane agriculture and integrated industry. These issues are land, fertility, water, variety, planting density, crop protection, cultural practices, harvesting and processing, and recently, computer information technology [1]. To all sugarcane farmers, it remains of top-most concern to grow the right cultivars. While it is the duty of conventional breeders to develop desirable sugarcane cultivars, biotechnologists can contribute greatly to the variety development process (crossing, selection, and evaluation) through the development and application of molecular breeding tools. Conventional sugarcane breeding is probably the most difficult job of any crop, due to the fact that sugarcane cultivars (Saccharum spp. hybrids) are highly polyploidy inter-specific hybrids containing 100 to 130 chromosomes [2,3]. The number of chromosomes may vary across geographical areas. Other obstacles/constraints include small flower size, the de...

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

“…In recent years, a number of different molecular marker systems have been developed for use in sugarcane, and SSRs have been shown to be the most powerful [10,13]. SSRs are sequence blocks containing DNA motifs of 1 to 6 base pairs repeated between 5-50 times and flanked by sequences that are generally unique in the genome, but conserved in organisms [10,14].…”

“…SSR-capillary electrophoresis/fluorescence detection (SSR-CE/FD) and fragment analysis by capillary electrophoresis are frequently used to overcome some of the aforementioned problems, and to identify higher numbers of polymorphic SSRs. These methods can develop a highly precise and effective SSR marker assay [5,13], even permitting a perfect and reproducible score for highly variable SSR loci. In contrast, other techniques, including lab gel electrophoresis techniques with silver or ethidium bromide staining, can cause allele miscalling due to stutters, primer dimers, and other PCR artifacts.…”

PIDS: A User-Friendly Plant DNA Fingerprint Database Management System

“…The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in determining kinship among individuals and in forensics to identify criminals [3][4][5][6]. In other applications, DNA fingerprints can provide accurate identification at the varieties level [7][8][9], and play important roles in plant breeding [10][11][12]. DNA fingerprints are also commonly used in research on animal evolutionary trends and animal varieties identification [8,13].…”

SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

“…Among PCR-based markers, SSR (microsatellite) markers are considered one of the most efficient markers for plant breeding due to large quantity, low dosage, co-dominant, reliability and multi-allelic detecting [22]. SSR markers have been used widely to study sugarcane genetic diversity and population structure [22][23][24], variety identity [25], genetic map [26,27], and genetic association [28][29][30]. Furthermore, fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) have manifested better performance in genotyping of polyploid sugarcane, due to higher accuracy and better detection power [22][23][24][31][32][33][34][35][36][37].…”