Databasing Molecular Identities of Sugarcane (Saccharum spp.) Clones Constructed with Microsatellite (SSR) DNA Markers

Pan, Yong‐Bao

doi:10.4236/ajps.2010.12011

Cited by 40 publications

(42 citation statements)

References 18 publications

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“…During this process, which involves the preparation of arrows (inflorescence) for crossing, seed processing, progeny planting at the field, might lead to exchange of progenies, mixing, and pollen or seed contamination. According to Pan (2010), the probability of error in the identification is considerably higher in clones or cultivars used as parents, which are propagated during several times over the years.…”

Section: Discussionmentioning

confidence: 99%

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Paternity identification in sugarcane polycrosses by using microsatellite markers

et al. 2014

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ABSTRACT. Although polycrosses have been used to test the potential of cross-combination of a large number of sugarcane parents, the male parent of the half-sib progenies produced is unknown. The present study aimed to integrate the molecular marker technology to the sugarcane polycross approach by the application of microsatellite markers to identify the male parent of 41 elite clones derived from polycross families. Ten microsatellite [single sequence repeats (SSRs)] primer pairs were used to identify the most likely male parent considering markers present in the selected clone but absent in the female parent. The number of alleles generated by the 10 microsatellite primer pairs ranged from 102 (cross-pollination lantern 4) to 120 (cross-pollination lantern 2) with an average of 113.25 alleles per SSR. The average genetic similarity among the involved parents in the polycrosses was 45.9%. The results of the analysis of the SSR markers absent in the female parent and present only in the selected clone as well as the genetic Paternity identification in sugarcane polycrosses similarity values allowed the identification of the most likely male parent in 73% of the total clones evaluated and also to detect probable contaminations. The obtained results highlight the importance of using molecular marker technology in the identification and confirmation of the male parent of high-performance clones derived from polycrosses in the sugarcane breeding programs.

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Section: Discussionmentioning

confidence: 99%

“…In all these applications, the most commonly used molecular markers are microsatellite markers (Pan, 2010).…”

Section: Introductionmentioning

confidence: 99%

Paternity identification in sugarcane polycrosses by using microsatellite markers

et al. 2014

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“…SSR markers have also been important in sugarcane genetic mapping studies Edme et al, 2006;Suman et al, 2011). To improve the efficiency of sugarcane breeding, some of the transferable SSR markers have been successfully used for molecular genotyping of sugarcane germplasm (Pan et al, , 2007, identification of hybrid progeny from interspecific crosses (Pan et al, 2006), paternity analysis of polycross progeny (Tew and Pan, 2010), and construction of a sugarcane molecular identity database (Pan, 2010).…”

Section: Introductionmentioning

confidence: 99%

Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

Lu¹,

Zhou²,

Pan³

et al. 2015

Genet. Mol. Res.

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ABSTRACT.No information is available on segregation analysis of DNA markers involving both pollen and self-progeny. Therefore, we used capillary electrophoresis-and fluorescence-based DNA fingerprinting together with single pollen collection and polymerase chain reaction (PCR) to investigate simple sequence repeat (SSR) marker segregation among 964 single pollens and 288 self-progenies (S 1 ) of sugarcane cultivar LCP 85-384. Twenty SSR DNA fragments (alleles) were amplified by five polymorphic SSR markers. Only one non-parental SSR allele was observed in 2392 PCRs. SSR allele inheritance was in accordance with Mendelian laws of segregation and independent assortment. Highly significant correlation coefficients were found between frequencies of observed and expected genotypes in pollen and S 1 populations. Within the S 1 population, the most frequent genotype of each SSR marker was the parental genotype of the same marker. The number of genotypes was higher in pollen than S 1 population. PIC values of the five SSR markers were greater in pollen than S 1 populations. Eleven of 20 SSR alleles (55%) were segregated in accordance with Mendelian segregation ratios expected from pollen and S 1 populations of a 2n = 10x polyploid. Six of 20 SSR alleles were segregated in a 3:1 (presence:absence) ratio and were simplex markers. Four and one alleles were segregated in 77:4 and 143:1 ratios and considered duplex and triplex markers, respectively. Segregation ratios of remaining alleles were unexplainable. The results provide information about selection of crossing parents, estimation of seedling population optimal size, and promotion of efficient selection, which may be valuable for sugarcane breeders.

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“…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.…”

mentioning

confidence: 99%

“…Other obstacles/constraints include small flower size, the development of the flower which may not synchronize between crossing parents, the likelihood of self-pollination, the difficulty in visually distinguishing F 1 hybrids from self progenies, the extreme genotypeˆenvironment or GˆE interactive effect, and potential variety mis-identification during vegetative propagation and varietal exchange, etc. [3,4]. It takes 12 to 14 years to develop a new sugarcane variety upon selection and evaluation against about 20 traits that include high tonnage, high sugar yield, early maturity, low fiber, harvest-ability, cold tolerance, ratooning ability, and resistance to a number of disease and insect pests [5].…”

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confidence: 99%

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

Pan

2016

Agronomy

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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...

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Databasing Molecular Identities of Sugarcane (Saccharum spp.) Clones Constructed with Microsatellite (SSR) DNA Markers

Abstract: ABSTRACT

Cited by 40 publications

References 18 publications

Paternity identification in sugarcane polycrosses by using microsatellite markers

Paternity identification in sugarcane polycrosses by using microsatellite markers

Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

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

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