scholarly journals Application of subtracted gDNA microarray-assisted Bulked Segregant Analysis for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa)

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Mian Chee Gor ◽  
Nitin Mantri ◽  
Edwin Pang
Keyword(s):  
Molecular Markers ◽  
Bulked Segregant Analysis ◽  
Fragaria X Ananassa

scholarly journals Bulked Segregant Analysis Identifies Molecular Markers Linked to Melampsora medusae Resistance in Populus deltoides

2000 ◽  
Vol 90 (9) ◽  
pp. 1039-1042 ◽  
Author(s):  
G. M. Tabor ◽  
T. L. Kubisiak ◽  
N. B. Klopfenstein ◽  
R. B. Hall ◽  
H. S. McNabb McNabb
Keyword(s):  
Molecular Markers ◽  
Leaf Rust ◽  
Populus Deltoides ◽  
Bulked Segregant Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Resistance Locus ◽  
The North ◽  
Melampsora Medusae ◽  
Central United States

In the north central United States, leaf rust caused by Melampsora medusae is a major disease problem on Populus deltoides. In this study we identified molecular markers linked to a M. medusae resistance locus (Lrd1) that was segregating 1:1 within an intraspecific P. deltoides family (C9425DD). Previous field results were confirmed in the controlled environment of a growth chamber through an excised whole-leaf inoculation method. Using bulked segregant analysis we identified two random amplified polymorphic DNA (RAPD) markers (OPG10340 and OPZ191800) that are linked to Lrd1. Based on segregation in a total of 116 progeny, the genetic distances between OPG10340 and OPZ191800 and the resistance locus were estimated as 2.6 and 7.4 Haldane centimorgans (cM), respectively. Multipoint linkage analyses strongly suggest the most likely order for these loci is Lrd1, OPG10340, and OPZ191800. These markers may prove to be instrumental in the eventual cloning of Lrd1, as well as for marker-assisted selection of leaf-rust resistant genotypes.

scholarly journals Bulked segregant analysis of the pirarucu (Arapaima gigas) genome for identification of sex-specific molecular markers

2013 ◽  
Vol 12 (4) ◽  
pp. 6299-6308 ◽  
Author(s):  
I.G. Almeida ◽  
P. Ianella ◽  
M.T. Faria ◽  
S.R. Paiva ◽  
A.R. Caetano
Keyword(s):  
Molecular Markers ◽  
Bulked Segregant Analysis ◽  
Arapaima Gigas

scholarly journals Analysis of strawberry genetic collection (Fragaria L.) for Rca2 and Rpfl genes with molecular markers

2018 ◽  
Vol 22 (7) ◽  
pp. 795-799 ◽  
Author(s):  
I. V. Luk’yanchuk ◽  
A. S. Lyzhin ◽  
I. I. Kozlova
Keyword(s):  
Molecular Markers ◽  
Genetic Distance ◽  
Resistance Gene ◽  
Wild Species ◽  
Root Rot ◽  
Scar Marker ◽  
Fragaria X Ananassa ◽  
Anthracnose Resistance ◽  
Monogenic Resistance ◽  
Red Stele

Strawberry (Fragaria x ananassa Duch.) varieties are susceptible to many fungal diseases. Identification of forms, carrying resistance genes, is an important stage in breeding programs leading to resistant varieties. The use of molecular markers allows to determine with high reliability the presence of the necessary genes in the genome and to identify promising forms. Some of the common strawberry's diseases, causing significant damage to strawberry plantations, are anthracnose (Colletotrichum acutatum Simmonds) and red stele root rot (Phytophthora fragariae var. fragariae Hickman). Dominant Rca2 gene is involved in monogenic resistance to C. acutatum pathogenicity group 2. Rpf1, Rpf2, Rpf3 genes are determined in monogenic resistance to red stele root rot. The purpose of this study was molecular genetic testing genotypes of genus Fragaria L. to identify carriers of Rca2 allele anthracnose resistance and Rpf1 allele red stele root rot resistance. The objects of study were the wild species of the genus Fragaria L. and strawberry varieties (Fragaria x ananassa Duch.) of different ecological and geographic origin. To assess allelic state Rca2 anthracnose resistance gene the dominant SCAR marker STS-Rca2_240 was used, was linked to the resistance gene Rca2 with a genetic distance of 2.8 cM. Rpf1 gene red stele root rot resistance was identified with the dominant SCAR marker R1A, was linked to the resistance gene Rpf1 with a genetic distance of 3.0 cM. The resistant allele of the marker STS-Rca2_240 was identified in the Laetitia variety (Rca2Rca2 or Rca2rca2 genotype), which allows us to recommend it as a promising source in breeding for anthracnose resistance. The other studied forms have homozygous recessive state of the marker STS-Rca2_240 (putative genotype rca2rca2). The resistant allele of the marker SCAR-R1A in the varieties and wild species of strawberry under study is absent, which presumably indicates their homozygous recessive genotype of Rpf1 gene (rpf1rpf1).

Molecular Markers Linked to Phytophthora fragariae Resistance Genes in Strawberry

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 500a-500 ◽  
Author(s):  
K.M. Haymes ◽  
S.C. Hokanson ◽  
K. Salazar ◽  
J. Maas
Keyword(s):  
Molecular Markers ◽  
Resistance Genes ◽  
Bulked Segregant Analysis ◽  
Aflp Markers ◽  
Avirulence Genes ◽  
Phytophthora Fragariae ◽  
Red Stele ◽  
Strawberry Breeding ◽  
Direct Applicability ◽  
Selection Of

The commercial strawberry (Fragaria × ananassa Duch.) is susceptible to red stele root rot caused by the fungus Phytophthora fragariae Hickman var. fragariae. Characteristics of the disease are the reddened steles and “rat tail” appearance of the roots. Infected plants are dwarfed, exhibit wilting, and eventually die. Red stele resistance in strawberries and virulence of P. fragariae behave according to the gene-for-gene system. Resistance genes and their corresponding avirulence genes have been identified by screening plant roots for infection. The goal of this international research project with CPRO-DLO, The Netherlands, is to develop highly specific molecular markers for various Rpf resistance genes (Rpf1, Rpf2, Rpf3, and Rpf6) that confer resistance against P. fragariae. Bulked Segregant Analysis was used to identify RAPD and AFLP markers putatively linked to P. fragariae resistance genes. The bulked DNAs representing subsets of three F1 populations that segregated monogenically for either resistance or susceptibility to P. fragariae. The map of these Rpf loci was generated using JoinMap®. The RAPD markers linked to the resistance genes are being converted into SCAR markers, while the AFLP markers will be used as probes for the detection of P. fragariae. The application of the molecular markers linked to resistance genes will have direct applicability to strawberry breeding programs. Marker-facilitated selection of these resistance genes would allow an efficient means in the screening and selection of plant material containing these genes and help in the pyramiding for resistance to P. fragariae. Genetic improvement of the strawberry by the ability to pyramid resistance genes will contribute to the productivity of the strawberry industry worldwide.

scholarly journals Screening of molecular markers linked to dwarf trait in crape myrtle by bulked segregant analysis

2015 ◽  
Vol 14 (2) ◽  
pp. 4369-4380 ◽  
Author(s):  
Y.J. Ye ◽  
Y. Liu ◽  
M. Cai ◽  
D. He ◽  
J.S. Shen ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Bulked Segregant Analysis

scholarly journals Unraveling genetics of semi-determinacy and identification of markers for indeterminate stem growth habit in chickpea (Cicer arietinum L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ambika ◽  
Venkatraman Hegde ◽  
M. S. Nimmy ◽  
C. Bharadwaj ◽  
Shailesh Tripathi ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Cicer Arietinum ◽  
Ssr Markers ◽  
Growth Habit ◽  
Bulked Segregant Analysis ◽  
Single Gene ◽  
Stem Growth ◽  
Segregation Pattern ◽  
Yield Potential ◽  
The Cross

AbstractChickpea (Cicer arietinum L.) is predominantly an indeterminate plant and tends to generate vegetative growth when the ambient is conducive for soil moisture, temperature and certain other environmental conditions. The semi-determinate (SDT) types are comparatively early, resistant to lodging and found to be similar in their yield potential to indeterminate (IDT) lines. Indeterminate and semi-determinate genotypes are found to be similar during early stage, which makes it difficult to distinguish between them. Thus, there is a need to identify molecular markers linked either to indeterminate or semi-determinate plant types. The present study was carried out to study the genetics of semi-determinacy and identify molecular markers linked to stem growth habit. The study was undertaken in the cross involving BG 362(IDT) × BG 3078-1(SDT). All F1 plants were indeterminate, which indicates that indeterminate stem type is dominant over semi-determinate. In further advancement to F2 generation, F2 plants are segregated in the ratio of 3(Indeterminate): 1(Semi-determinate) that indicates that the IDT and SDT parents which are involved in the cross differed for a single gene. The segregation pattern observed in F2 is confirmed in F3 generation. The parental polymorphic survey was undertaken for molecular analysis using total of 245 SSR markers, out of which 41 polymorphic markers were found to distinguish the parents and were utilized for bulked segregant analysis (BSA). The segregation pattern in F2 indicates that the IDT (Indeterminate) and SDT (Semi-determinate) parents which are involved in the cross differed for single gene. The segregation pattern of F2 and F3 derived from the cross BG 362 (IDT) × BG 3078-1 (SDT) confirmed the genotypic structure of the newly found SDT genotype BG 3078-1 as dt1dt1Dt2Dt2. Three SSR markers TA42, Ca_GPSSR00560 and H3DO5 were found to be putatively linked to Dt1 locus regulating IDT stem growth habit. Our results indicate that the SSR markers identified for Dt1 locus helps to differentiate stem growth habit of chickpea in its early growth stage itself and can be efficiently utilized in Marker Assisted Selection (MAS) for changed plant type in chickpea.

scholarly journals Genetic variations of strawberry cultivars of Fragaria x ananassa and Fragaria vesca based on RAPD

2019 ◽  
Vol 20 (3) ◽  
pp. 770-775
Author(s):  
GANIES RIZA ARISTYA ◽  
RINA SRI KASIAMDARI ◽  
RACHMI SETYONINGRUM ◽  
BENING LARASATI
Keyword(s):  
Genetic Variation ◽  
Molecular Markers ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Index ◽  
Dna Amplification ◽  
Genetic Variations ◽  
Fragaria X Ananassa ◽  
Fragaria Vesca ◽  
Market Demand ◽  
Strawberry Cultivars

Abstract. Aristya GR, Kasiamdari RS, Setyoningrum R, Larasati B. 2019. Genetic variations of strawberry cultivars of Fragaria x ananassa and Fragaria vesca based on RAPD. Biodiversitas 20: 770-775. In Indonesia, the increasing market demand for strawberries (Fragaria spp.) is not comparable to increased strawberry productivity. One of the efforts made to increase strawberry productivity with superior quality is plant breeding. The purpose of this research was to determine the genetic variation, lineage, and similarity index in some strawberry cultivars using molecular markers of Random Amplified Polymorphic DNA (RAPD). Eleven strawberry cultivar samples were taken from Indonesian Citrus and Subtropical Fruits Research Institute (Balitjestro), Batu City, East Java, Indonesia and Strawberry Agritourism in Banyuroto Village, Magelang District, Central Java, Indonesia. DNA isolation using modified CTAB buffer method. DNA amplification using PCR-RAPD method with 5 primers, namely UBC-516, UBC-594, OPA 10, OPA 16, and OPG 11. Strawberry lineage dendrogram construction was analyzed with clustering of Unweight Pair-Group Using Arithmetic Average (UPGMA) software Multi-Variate Statistical Average (MVSP). The research results showed that the 5 RAPD primers used in 11 strawberry cultivars produced 30 polymorphic DNA bands and 20 monomorphic DNA bands so it can be concluded that the genetic variation among 11 strawberry cultivars can be detected using RAPD molecular markers. The lineage of 11 strawberry cultivars that have the highest similarity index is found in Earlibrite and Rosalinda II cultivars of 98.85%.

A molecular marker closely linked to the region of Rht-D1c and Ms2 genes in common wheat (Triticum aestivum)

Genome ◽  
2009 ◽  
Vol 52 (1) ◽  
pp. 95-99 ◽  
Author(s):  
Wenguang Cao ◽  
Daryl J. Somers ◽  
George Fedak
Keyword(s):  
Triticum Aestivum ◽  
Molecular Markers ◽  
Molecular Marker ◽  
Male Sterility ◽  
Common Wheat ◽  
Recurrent Selection ◽  
Bulked Segregant Analysis ◽  
Dominant Gene ◽  
Male Sterile ◽  
Dwarfing Gene

A male sterile wheat mutant, Triticum aestivum L. ‘Taigu’, was found in a wheat field in China in 1972. The male sterility was controlled by a single dominant gene that was referred to as Ms2. Recently, this gene was found to be linked to a dwarfing gene through crossing Taigu with the short wheat T. aestivum ‘Ai-Bian 1’ carrying the dwarfing gene Rht-D1c. The objective of this study was to develop molecular markers linked to the male sterility Ms2 gene in common wheat. One hundred and twenty-two near-isogenic lines were developed through backcrossing and sib intercrossing and used as the mapping population for the development of molecular markers. Bulked segregant analysis was used to screen 48 pairs of SSR primers, and a marker, MS2-WMC617, was identified closely linked to the male sterile Ms2 gene that mapped at the distal position of chromosome arm 4DS. The use of the molecular marker MS2-WMC617 can facilitate recurrent selection in a wheat breeding program based on marker-assisted selection.

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