SSR marker-based analysis of genetic relatedness among sugarcane cultivars (Saccharum spp. hybrids) from breeding programs in China and other countries

Sugar Tech ◽  
2009 ◽  
Vol 11 (4) ◽  
pp. 347-354 ◽  
Author(s):  
P. H. Chen ◽  
Y. -B. Pan ◽  
R. -K. Chen ◽  
L. -P. Xu ◽  
Y. -Q. Chen
Keyword(s):  
Ssr Marker ◽  
Genetic Relatedness ◽  
Breeding Programs ◽  
Saccharum Spp

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

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 449 ◽  
Author(s):  
Jiantao Wu ◽  
Qinnan Wang ◽  
Jing Xie ◽  
Yong-Bao Pan ◽  
Feng Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Capillary Electrophoresis ◽  
Population Structure ◽  
Ssr Markers ◽  
High Performance ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Parental Lines ◽  
Assisted Management ◽  
High Performance Capillary Electrophoresis

Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (Fst) value and gene flow (Nm) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s).

scholarly journals Physical purity and germination of sugarcane seeds (caryopses) (Saccharum spp.)

2010 ◽  
Vol 32 (2) ◽  
pp. 140-145 ◽  
Author(s):  
Juliana Terezinha Caieiro ◽  
Maristela Panobianco ◽  
João Carlos Bespalhok Filho ◽  
Osvaldo de Castro Ohlson
Keyword(s):  
Plant Breeding ◽  
Seed Viability ◽  
Germination Test ◽  
Paper Substrate ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Test Study ◽  
Alternating Temperature ◽  
Incubation Temperatures ◽  
Favorable Conditions

Plant breeding is generally done through sexual reproduction even when the species is propagated asexually for commercial exploitation, as for example, in sugarcane. Therefore, the development of procedures to evaluate sugarcane seed viability is important for plant breeding programs. The objective of this research was to develop a methodology for analyzing the viability of sugarcane seeds (Saccharum spp.). Three crosses were used, two biparental crosses and one polycross. For the germination test study, two substrates (paper and sand) and three constant incubation temperatures (25 ºC, 30 ºC and 35 ºC), in the presence of constant light and also an alternating temperatures (20-30 ºC), with 8 hours light (30 ºC) and 16 hours darkness (20 ºC), were studied. Seedlings were evaluated every five days. The results demonstrated that temperature affected sugarcane seed germination with the most favorable conditions being the alternating temperature (20-30 ºC) and the constant temperature of 30 ºC on a paper substrate.

Development and characterization of EST-SSR markers from Jatropha curcas EST database and their transferability across jatropha-related species/genus

Biologia ◽  
2013 ◽  
Vol 68 (1) ◽  
Author(s):  
Kularb Laosatit ◽  
Patcharin Tanya ◽  
Chatree Saensuk ◽  
Peerasak Srinives
Keyword(s):  
Ssr Markers ◽  
Jatropha Curcas ◽  
Related Species ◽  
High Efficiency ◽  
Genetic Relatedness ◽  
Ricinus Communis ◽  
Raw Material ◽  
Breeding Programs ◽  
New Varieties

AbstractJatropha curcas (jatropha) is a multipurpose plant with potential as a raw material for biofuel. In the present study, a total of 43,349 expressed sequence tags (ESTs) from J. curcas were searched for type and frequency of simple sequence repeat (SSR) markers. Five thousand one hundred and seventy-five sequences were indentified to contain 6,108 SSRs with 90.8% simple and 9.2% compound repeat motifs. One hundred and sixty-three EST-SSRs were developed and used to evaluate the transferability and genetic relatedness among 4 accessions of J. curcas from China, Mexico, Thailand and Vietnam; 5 accessions of congeneric species, viz. J. gossypiifolia, dwarf J. integerrima, normal J. integerrima, J. multifida, J. podagrica; and Ricinus communis. The polymorphic markers showed 75.56–85.19% transferability among four species of Jatropha and 26.67% transferability across genera in Ricinus communis. Investigation of genetic relatedness showed that J. curcas and J. integerrima are closely related. EST-SSRs used in this study demonstrate a high efficiency of cross species/genera amplification and are useful for identifying genetic diversity of jatropha and its close taxa and to choose the desired related species for wide crossing to improve new varieties of jatropha. The markers can also be further exploited for genetic resource management and genetic improvement of related species/genera through marker-assisted breeding programs.

scholarly journals The Design of Early-Stage Plant Breeding Trials Using Genetic Relatedness

2020 ◽  
Vol 25 (4) ◽  
pp. 553-578 ◽  
Author(s):  
Brian R. Cullis ◽  
Alison B. Smith ◽  
Nicole A. Cocks ◽  
David G. Butler
Keyword(s):  
Plant Breeding ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Genetic Relatedness ◽  
Early Stage ◽  
Genetic Effects ◽  
Breeding Programs ◽  
Model Based ◽  
Selection Decisions ◽  
Design Generation

Abstract The use of appropriate statistical methods has a key role in improving the accuracy of selection decisions in a plant breeding program. This is particularly important in the early stages of testing in which selections are based on data from a limited number of field trials that include large numbers of breeding lines with minimal replication. The method of analysis currently recommended for early-stage trials in Australia involves a linear mixed model that includes genetic relatedness via ancestral information: non-genetic effects that reflect the experimental design and a residual model that accommodates spatial dependence. Such analyses have been widely accepted as they have been found to produce accurate predictions of both additive and total genetic effects, the latter providing the basis for selection decisions. In this paper, we present the results of a case study of 34 early-stage trials to demonstrate this type of analysis and to reinforce the importance of including information on genetic relatedness. In addition to the application of a superior method of analysis, it is also critical to ensure the use of sound experimental designs. Recently, model-based designs have become popular in Australian plant breeding programs. Within this paradigm, the design search would ideally be based on a linear mixed model that matches, as closely as possible, the model used for analysis. Therefore, in this paper, we propose the use of models for design generation that include information on genetic relatedness and also include non-genetic and residual models based on the analysis of historic data for individual breeding programs. At present, the most commonly used design generation model omits genetic relatedness information and uses non-genetic and residual models that are supplied as default models in the associated software packages. The major reasons for this are that preexisting software is unacceptably slow for designs incorporating genetic relatedness and the accuracy gains resulting from the use of genetic relatedness have not been quantified. Both of these issues are addressed in the current paper. An updating scheme for calculating the optimality criterion in the design search is presented and is shown to afford prodigious computational savings. An in silico study that compares three types of design function across a range of ancillary treatments shows the gains in accuracy for the prediction of total genetic effects (and thence selection) achieved from model-based designs using genetic relatedness and program specific non-genetic and residual models. Supplementary materials accompanying this paper appear online.

scholarly journals Genetic diversity and population structure of sugarcane (Saccharum spp.) accessions by means of microsatellites markers

2020 ◽  
Vol 42 ◽  
pp. e45088
Author(s):  
Hugo Zeni Neto ◽  
Luiz Gustavo da Mata Borsuk ◽  
Luiz Renato Frederico dos Santos ◽  
Henrique Sanches Angeli ◽  
Guilherme Souza Berton ◽  
...  
Keyword(s):  
Population Structure ◽  
Probabilistic Models ◽  
Similarity Coefficient ◽  
Group Method ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Pair Group ◽  
Industrial Yield ◽  
Degree Of Similarity ◽  
Simple Sequence

The success of sugarcane (Saccharum spp.) breeding programs depends on the choice of productive parent lines that have a high industrial yield and are genetically divergent. This study assessed the genetic divergence and population structure of sugarcane accessions that are the parents of the RB05 Series of the Sugarcane Breeding Program of Brazil. The DNA of 82 accessions was evaluated using 36 simple sequence repeat markers. The Jaccard similarity coefficient and Unweighted Pair Group Method with Arithmetic Mean clustering method were used to generate a cluster that was divided into 17 distinct groups derived from probabilistic models. The similarity coefficient used in both cases showed that the degree of similarity varied from 0.4716 (RB971551 x RB965586) to 0.9526 (RB936001 x SP89-1115), with a mean of 0.8536. This result demonstrates a high similarity between the 82 accessions and confirms Wright’s F statistic (0.125), which indicates moderate genetic variability. The less-similar crosses suggest that breeders seek a higher number of crosses using cultivar RB965586, highlighting the RB971551 x RB965586 and RB965586 x RB855511 crosses. The results demonstrate that crosses such as RB936001 x SP89-1115 and RB945954 x RB896342 should be avoided because of their high genetic similarity.

Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data

Genome ◽  
2007 ◽  
Vol 50 (4) ◽  
pp. 373-384 ◽  
Author(s):  
M. Maccaferri ◽  
S. Stefanelli ◽  
F. Rotondo ◽  
R. Tuberosa ◽  
M.C. Sanguineti
Keyword(s):  
Durum Wheat ◽  
Genetic Relatedness ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Phenotypic Traits ◽  
Pedigree Data ◽  
Crop Species ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Triticum Durum Desf

The determination of genetic relatedness among elite materials of crop species allows for more efficient management of breeding programs and for the protection of breeders’ rights. Seventy simple sequence repeats (SSRs) and 234 amplified fragment length polymorphisms (AFLPs) were used to profile a collection of 58 durum wheat ( Triticum durum Desf.) accessions, representing the most important extant breeding programs. In addition, 42 phenotypic traits, including the morphological characteristics recommended for the official distinctness, uniformity, and stability tests, were recorded. The correlation between the genetic similarities obtained with the 2 marker classes was high (r = 0.81), whereas lower values were observed between molecular and phenotypic data (r = 0.46 and 0.56 for AFLPs and SSRs, respectively). Morphological data, even if sampled in high numbers, largely failed to describe the pattern of genetic similarity, according to known pedigree data and the indications provided by molecular markers.

scholarly journals Genetic variation and characterization of the sucrose synthase 2 gene (Sus2) in sugarcane based molecular markers

2019 ◽  
Vol 20 (11) ◽  
Author(s):  
RINA SRI KASIAMDARI ◽  
DEA FEBIANSI ◽  
HERI PRABOWO ◽  
Ganies Riza Aristya ◽  
ARNI MUSTHOFA
Keyword(s):  
Genetic Variation ◽  
Molecular Markers ◽  
Sucrose Synthase ◽  
Similarity Index ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Gene Level ◽  
Analysis Of Variation ◽  
Large Clusters

Abstract. Kasiamdari RS, Febiansi D, Prabowo H, Aristya GR, Musthofa A. 2019. Genetic variation and characterization of the sucrose synthase 2 gene (Sus2) in sugarcane based molecular markers. Biodiversitas 20: 3087-3096. Sugarcane (Saccharum spp.) genotype is one of the sugar-producing plants and an important commodity to support the community’s economy. Plant breeders continuously cross-breed these plants to obtain cultivars with desirable traits to produce a variety of new phenotypes. An analysis of variation at gene-level is carried out as an important step in plant breeding programs. The purpose of the present study was to determine genetic variation and characterize the sucrose synthase 2 gene (Sus2) based on molecular markers. Twenty sugarcane cultivars were sampled from Indonesian Sweetener and Fiber Crops Research Institute (BALITTAS) Malang and four sugarcane cultivars from PT. Madu Baru in Polosio A Plantation, Poncosari, Srandakan, Bantul Regency, Yogyakarta. DNAs were amplified using two primer pairs, i.e. AI and SMC226CG. The genetic variations of the twenty-four sugarcane cultivars were analyzed by constructing a dendrogram of the Amplified DNA using Multi-Variate Statistical Package (MVSP) software. The results showed that there were three large clusters, namely Cluster A consisting of ‘PS 865’, ‘PS 951’, ‘PS 921’, and ‘PS 58’, with a similarity index of 57%; Cluster B consisting of the sugarcane ‘Kentung’, with a similarity index of 33%; and cluster C consisting of the sugarcane ‘PSDK 923’, ‘PSBM 901’, ‘TLH 2’, ‘BL’, ‘PSJT 941’, ‘KK’, ‘PS 80.1649’, ‘PSCO 902’, ‘PS 80,910’, ‘PS 882’, ‘PS 862’, ‘PS 851’, ‘PS 881’, ‘PS 865’, ‘PS 384’, ‘VMC 76-16’, ‘BZ 132’, ‘PS 891’, ‘PS 41’ with a similarity index of 60%. Polymorphisms occurred after the DNAs were amplified and after the bands appeared in heterozygous and homozygous individuals. In sugarcane, the Sus2 gene when detected by the molecular marker primer AI showed high-sucrose sugarcane; whereas the Sus2 gene detected by the primer SMC226CG showed low-sucrose sugarcane. Results of the present study showed that all sugarcane samples were detected as having low sucrose except Bulu Lawang and Kentung cultivars.

scholarly journals Field resistance and molecular detection of the orange rust resistance gene linked to G1 marker in Brazilian cultivars of sugarcane

2020 ◽  
Vol 46 (2) ◽  
pp. 92-97 ◽  
Author(s):  
Ícaro Fier ◽  
Thiago Willian Almeida Balsalobre ◽  
Roberto Giacomini Chapola ◽  
Hermann Paulo Hoffmann ◽  
Monalisa Sampaio Carneiro
Keyword(s):  
Molecular Detection ◽  
Durable Resistance ◽  
Marker Locus ◽  
Field Resistance ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Resistant Phenotype ◽  
Marker Efficiency ◽  
Diagrammatic Scale ◽  
Sugarcane Industry

ABSTRACT Sugarcane (Saccharum spp.), an important crop for tropical and subtropical countries, is used in the production of sugar and biofuel. Orange rust, a disease caused by the fungus Puccinia kuehnii, can reduce the yield and harm the sugarcane industry. Molecular markers linked to resistance genes can help breeding programs confirm introgression of favorable alleles, find new resistance sources and release new cultivars that have durable resistance. In the current study, the aims were (i) to evaluate in the field the resistance to orange rust of 24 Brazilian commercial cultivars; (ii) to assess the frequency of the allele at G1 marker locus in the set of cultivars, and (iii) to study the usefulness of G1 marker to predict the resistant phenotype and its potential for marker assisted selection. A diagrammatic scale, which ranged from 1 (plants without symptoms) to 9 (highly susceptible plants), was used to determine the disease severity. Considering resistant cultivars those with mean severity up to 3, G1 marker efficiency in predicting the resistant phenotype was 71.43%. In addition, there was a reduction of 35% in the overall mean severity when G1 marker was present. G1 marker is an important molecular tool that can be used by breeding programs in the search for sugarcane cultivars resistant to orange rust.

scholarly journals Polymorphic Identification of Simple Sequence Repeat (SSR) Marker for Developing Aluminum-Tolerance Upland Rice

2020 ◽  
Vol 5 (1) ◽  
pp. 50-62
Author(s):  
Yuliana Galih Dyan Anggraheni ◽  
Enung Sri Mulyaningsih ◽  
Dody Priadi ◽  
Puspita Deswina ◽  
Yuli Sulistyowati ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Ssr Marker ◽  
Upland Rice ◽  
Aluminum Tolerance ◽  
Al Tolerance ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Ssr Primers ◽  
And Control ◽  
Selection Of

SSR marker is one of the genetic markers widely applied in plant breeding programs. The application of molecular markers in plant breeding is meant to accelerate the selection of cross-progeny. The research aimed to identify the SSR primers polymorphism between the parent and control that linked to Al tolerance and verify the cross-progeny of five crosses. The result gained from 37 SSR primers used in this study showed that only nine primers are polymorphic. These nine polymorphic primers are RM257, RM214, RM247, RM205, RM490, RM262, RM569, RM271, and RM19. The application of polymorphic markers on five cross-progeny which have shown the same band pattern as the parents and tolerant control on the use of 9 SSR primers recorded as follows: RM257 2 lines, RM214 5 lines, RM247 5 lines, RM205 lines, RM490 13 lines, RM262 5 lines, RM569 7 lines, RM271 4 lines, and RM19 6 lines. The selected SSR primers linked to Al tolerance in this research can be used as a reference for molecular breeding strategies to develop new Al tolerance rice varieties in dryland conditions.

Genetic Relatedness of Pecan Cultivars Determined by Using Random Amplified Polymorphic DNA (RAPD)

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 493b-493
Author(s):  
Yongling Xiao ◽  
Dong Young Shin ◽  
Hazel Y. Wetzstein
Keyword(s):  
Genetic Variation ◽  
Genomic Dna ◽  
Genetic Relatedness ◽  
Random Amplified Polymorphic Dna ◽  
Breeding Programs ◽  
Parent Selection ◽  
Cultivar Classification

Although pecan (Carya illinoinensis) is an economically important nut and timber crop, little is known about the nature of genetic variation among pecan cultivars. In addition, the pedigree of many cultivars remains unknown or is questionable. In this study, the genomic DNA of 20 pecan cultivars were analyzed by RAPD, using 20 randomly selected oligoes as primers. Based on their genetic similarities derived from the RAPD data, the 20 pecan cultivars were classified into different groups. Pecan cultivars within the same group displayed very little genetic variation, whereas cultivars in different groups showed significant diversity. The putative origins for some pecan cultivars previously believed to have unknown pedigrees were also identified based on the RAPD data obtained. Results of this study provide information useful for pecan cultivar classification and parent selection in pecan breeding programs.

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