Identification of SSR marker associated with rust resistance in cowpea (Vigna unguiculata L.) using bulk segregant analysis

2016 ◽  
Vol 39 (1) ◽  
Author(s):  
M. S. Uma ◽  
Niranjan Hegde ◽  
Shailaja Hittalmani
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Rust Resistance ◽  
Bulked Segregant Analysis ◽  
Rust Disease ◽  
Ssr Primers ◽  
Single Marker ◽  
Significant Regression ◽  
Resistant Genotypes ◽  
Selection Of

Bulked segregant analysis was undertaken to tag gene(s) controlling rust resistance using molecular markers in cowpea, to permit rapid selection of superior desirable rust resistant genotypes in the breeding program. For this purpose, the C-152, cultivated variety with high yielding, semi determinate plant type, good protein content and highly rust susceptible was crossed with genotype IC202778, the landrace from Himachal Pradesh, India having determinate, semi spreading and rust resistant characters. The parental genotypes were analyzed with 92 SSR markers for detection of polymorphism and only 13 markers showed polymorphism between the parents. Using each of these 13 SSR primers, we carried out bulked segregate analysis on F<sub>2</sub> plants representing two extremes of rust disease resistance and susceptible trait. Three SSR markers VuUGM02, VuUGM08 and VuUGM19 were found to be associated with rust resistance. This was further confirmed through selective genotyping. The co-segregation data on these molecular markers and rust resistance on F<sub>2</sub> plants were analysed by means of single-marker linear regression approach. Significant regression suggested linkage between VuUGM02 and rust resistance gene.

scholarly journals Detection of QTL associated with rust resistance using IBD-based methodologies in exogamic Eucalyptus spp. populations

2010 ◽  
Vol 10 (4) ◽  
pp. 321-328 ◽  
Author(s):  
Tatiana Barbosa Rosado ◽  
Rafael Simões Tomaz ◽  
Marcio Fernandes Ribeiro Junior ◽  
Antônio Marcos Rosado ◽  
Lúcio Mauro da Silva Guimarães ◽  
...  
Keyword(s):  
Rust Resistance ◽  
Control Method ◽  
Interval Mapping ◽  
Single Marker Analysis ◽  
Mapping Procedure ◽  
Integrated Map ◽  
Single Marker ◽  
Resistant Genotypes ◽  
Important Disease ◽  
Selection Of

In Brazil the rust caused by Puccinia psidii Winter stands out as the most important disease of eucalyptus. The use of resistant genotypes is the main control method, which makes the detection of markers linked to rust resistance essential to the selection of resistant genotypes. In this study, an F1 progeny of 131 plants from interspecific crossings of Eucalyptus was used to identify markers linked to resistance genes for this pathogen. An integrated map was constructed for linkage group three based on microsatellite markers. For QTL mapping two methodologies based on alleles identical-by-descent (IBD) were used: single marker analysis of Haseman and Elston and the interval mapping procedure of Fulker and Cardon. Both methods showed significant association for the Embra 125 marker.The QTL that explained 42 % of the phenotypic variation was mapped to 0.02 cM of this marker by the Fulker and Cardon. Marker Embra 125 has potential use in assisted selection, thus increasing the efficiency of the selection of resistant genotypes.

scholarly journals Confirmation of Alleles Inheritance in F1 Progenies Derived from a Cross of Calcutta-4 [Musa acuminata ssp. burmannicoides] and Musa acuminata ssp. microcarpa Based on SSR Markers

2020 ◽  
Vol 16 (1) ◽  
pp. 17
Author(s):  
Dea Rosalia ◽  
Puji Lestari ◽  
Andy Soegianto ◽  
Darmawan Saptadi ◽  
Agus Sutanto ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Disease Resistance ◽  
Ssr Markers ◽  
Selection Process ◽  
Musa Acuminata ◽  
Chi Square ◽  
Genetic Studies ◽  
Ssr Primers ◽  
Chi Square Analysis ◽  
Selection Of

<p>Banana breeding to produce improved varieties with disease resistance haracters and other desired traits could sustain its yield. Alleles harbored by parents could be passed on to the offsprings through hybridization, but need to be confirmed using molecular markers. This study aimed to confirm allele inheritance in F1 progenies derived from a cross of Calcutta-4 (Musa acuminata ssp.  burmannicoides) and M. acuminata ssp. microcarpa based on SSR markers. Eleven pairs of SSR primers were used to amplify DNA of 44 progenies using the PCR technique. The results showed that six SSR markers (MaSSR 1.1, MaSSR<br />5.1, MaSSR 6.1, MaSSR 7.1, MaSSR 8.1, and MaSSR 11.1) were polymorphic in both parents. Four markers (MaSSR 1.1, MaSSR 5.1, MaSSR 6.1, and MaSSR 8.1) had PIC &gt;0.7, indicating their informativeness to distinguish these progenies and other genetic studies of banana germplasms. A total of 44 F1 individuals were confirmed to harbor alleles inherited from their parents,<br />suggesting as true progenies from the cross of Calcutta-4 and M. acuminata ssp. microcarpa. This population demonstrated 100% success of hybridization performed. Chi-Square analysis revealed that segregation of all markers did not match to Mendelian ratio 1:2:1, except for MaSSR 1.1 (x2 = 5,62) and MaSSR 6.1 (x2 = 3,77) markers. The genetic traceability of banana F1 progenies demonstrating the usefulness and feasibility of SSR markers in this study provided information on selection of true progenies which may be valuable for breeders to assist selection process in future banana breeding program in Indonesia.</p>

scholarly journals Combining Single Nucleotide Polymorphism Genotyping Array with Bulked Segregant Analysis to Map a Gene Controlling Adult Plant Resistance to Stripe Rust in Wheat Line 03031-1-5 H62

2018 ◽  
Vol 108 (1) ◽  
pp. 103-113 ◽  
Author(s):  
Jianhui Wu ◽  
Qilin Wang ◽  
Liangsheng Xu ◽  
Xianming Chen ◽  
Bei Li ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Bulked Segregant Analysis ◽  
Snp Array ◽  
Adult Plant ◽  
Wheat Line ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Kasp Markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating diseases of wheat worldwide. Growing resistant cultivars is considered the best approach to manage this disease. In order to identify the resistance gene(s) in wheat line 03031-1-5 H62, which displayed high resistance to stripe rust at adult plant stage, a cross was made between 03031-1-5 H62 and susceptible cultivar Avocet S. The mapping population was tested with Chinese P. striiformis f. sp. tritici race CYR32 through artificial inoculation in a field in Yangling, Shaanxi Province and under natural infection in Tianshui, Gansu Province. The segregation ratios indicated that the resistance was conferred by a single dominant gene, temporarily designated as YrH62. A combination of bulked segregant analysis (BSA) with wheat 90K single nucleotide polymorphism (SNP) array was used to identify molecular markers linked to YrH62. A total of 376 polymorphic SNP loci identified from the BSA analysis were located on chromosome 1B, from which 35 kompetitive allele-specific PCR (KASP) markers selected together with 84 simple sequence repeat (SSR) markers on 1B were used to screen polymorphism and a chromosome region associated with rust resistance was identified. To saturate the chromosomal region covering the YrH62 locus, a 660K SNP array was used to identify more SNP markers. To develop tightly linked markers for marker-assisted selection of YrH62 in wheat breeding, 18 SNPs were converted into KASP markers. A final linkage map consisting of 15 KASP and 3 SSR markers was constructed with KASP markers AX-109352427 and AX-109862469 flanking the YrH62 locus in a 1.0 cM interval. YrH62 explained 63.8 and 69.3% of the phenotypic variation for disease severity and infection type, respectively. YrH62 was located near the centromeric region of chromosome 1BS based on the positions of the SSR markers in 1B deletion bins. Based on the origin, responses to P. striiformis f. sp. tritici races, and marker distances, YrH62 is likely different from the other reported stripe rust resistance genes/quantitative trait loci on 1B. The gene and tightly linked KASP markers will be useful for breeding wheat cultivars with resistance to stripe rust.

scholarly journals Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L.) obtained by RAPD and SSR markers

2008 ◽  
Vol 51 (1) ◽  
pp. 183-192 ◽  
Author(s):  
Silvia Graciele Hülse de Souza ◽  
Valéria Carpentieri-Pípolo ◽  
Claudete de Fátima Ruas ◽  
Valdemar de Paula Carvalho ◽  
Paulo Maurício Ruas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Zea Mays L ◽  
Inbred Lines ◽  
Pedigree Data ◽  
Dice Coefficient ◽  
Quantitative Characters ◽  
Maize Inbred Lines ◽  
Ssr Primers ◽  
Selection Of

The RAPD and SSR markers were used to compare the genetic diversity among the 16 maize inbred lines. Twenty-two primers were used in the RAPD reactions, resulting in the amplification of 265 fragments, while 16 pairs of SSR primers resulted in 75 fragments. The similarity based on Dice coefficient for the RAPD ranged from 53 to 84% and for the SSR from 11 to 82%. The dendrogram obtained by the RAPD showed five groups, while dendrogram obtained by the SSR showed three groups and one isolated line. The association constructed from the markers and the principal coordinate’s analysis separated lines into two groups according to endosperm color, either orange or yellow. The RAPD were effective to validate pedigree data, while the SSR were effective to recognize the differences between the quantitative characters. Because they assess the distinct regions of the genome, the selection of one or other marker would depend on the characteristics of the material used and the objectives of the project.

scholarly journals Identification of Putative Molecular Markers Associated with Nut Weight and Kernel Weight and Four Growth Traits in Cashew

2020 ◽  
pp. 262-274
Author(s):  
E. Eradasappa ◽  
G. S. Mohana ◽  
J. D. Adiga ◽  
Siddanna Savadi
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Growth Traits ◽  
Tree Height ◽  
Kernel Weight ◽  
Growth And Yield ◽  
Phenotypic Variance ◽  
Single Marker Analysis ◽  
Marker Analysis ◽  
Single Marker

Aim: To identify putative molecular markers linked to some useful traits in cashew using SSR markers in the F1 population. Place and Duration of the Study: Study conducted at ICAR-Directorate of Cashew Research, Puttur, Karnataka, India during 2013-17. Methodology: Population for the study comprised of 83 F1 plants developed through crossing tall variety Ullal-3 as female parent with dwarf accession NRC-492 as male parent which was planted in the field at 6m x 6m spacing during the year 2009. It was phenotyped along with parents during the year 2017 for the 13 growth and yield related traits and genotyped using 32 polymorphic SSR markers from cashew, almond, pistachio and mango. Single marker analysis was deployed to identify the markers linked to traits by SPSS software. Results: results revealed three markers such as AL 29, IM 31 and IM 28 to be significantly associated with some traits. Marker AL 29 from Almond species was linked to traits stem girth, nut weight and kernel weight with an explained phenotypic variance of 7.9%, 5.6% and 5.4%, respectively. Marker IM 31 from mango species was associated with stem girth, kernel weight, tree height, mean tree spread, nut weight and presented phenotypic variance of 17.6%, 5.7%, 8.2%, 4.5, 4.2% in that order. While the marker IM 28 from mango species showed linked with stem girth and intermodal length with phenotypic variance of 7.6%, 7.5%, 10.4% correspondingly. Conclusion: The present study has identified three markers AL 29  (from Almond) , IM 28 and IM  31 (from Mango) linked to six traits viz., stem girth, tree height, mean tree spread, intermodal length, nut weight and kernel weight with the limited polymorphic markers using Single Marker Analysis. However, further studies are aimed to validate the linked markers prior to using them in marker assisted selection in cashew.

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.

Targeting test environments and rust-resistant genotypes in lentils (Lens culinaris) by using heritability-adjusted biplot analysis

2018 ◽  
Vol 69 (11) ◽  
pp. 1113 ◽  
Author(s):  
A. K. Parihar ◽  
Ashwani K. Basandrai ◽  
K. P. S. Kushwaha ◽  
S. Chandra ◽  
K. D. Singh ◽  
...  
Keyword(s):  
Lens Culinaris ◽  
Rust Resistance ◽  
High Efficiency ◽  
Environment Interaction ◽  
Gge Biplot ◽  
Rust Disease ◽  
Ge Interaction ◽  
Sources Of Resistance ◽  
Biplot Analysis ◽  
Resistant Genotypes

Lentil rust incited by the fungus Uromyces viciae-fabae is a major impedance to lentil (Lens culinaris Medik.) production globally. Host-plant resistance is the most reliable, efficient and viable strategy among the various approaches to control this disease. In this study, 26 lentil genotypes comprising advanced breeding lines and released varieties along with a susceptible check were evaluated consecutively for rust resistance under natural incidence for two years and at five test locations in India. A heritability-adjusted genotype main effect plus genotype × environment interaction (HA-GGE) biplot program was used to analyse disease-severity data. The results revealed that, among the interactive factors, the GE interaction had the greatest impact (27.81%), whereas environment and genotype showed lower effects of 17.2% and 20.98%, respectively. The high GE variation made possible the evaluation of the genotypes at different test locations. The HA-GGE biplot method identified two sites (Gurdaspur and Pantnagar) as the ideal test environments in this study, with high efficiency for selection of durable and rust-resistant genotypes, whereas two other sites (Kanpur and Faizabad) were the least desirable test environments. In addition, the HA-GGE biplot analysis identified three distinct mega-environments for rust severity in India. Furthermore, the analysis identified three genotypes, DPL 62, PL 165 and PL 157, as best performing and durable for rust resistance in this study. The HA-GGE biplot analysis recognised the best test environments, restructured the ecological zones for lentil-rust testing, and identified stable sources of resistance for lentil rust disease, under multi-location and multi-year trials.

scholarly journals Lokus SSR Berasosiasi Karakter Tahan Penyakit Mati-Pohon Durian Berdasarkan Bulked Pseudo-Segregant Analysis (SSR Loci Associated to Resistance Traits to Durian Die-Back based on Bulked Pseudo-Segregant Analysis)

2020 ◽  
Vol 30 (1) ◽  
pp. 9
Author(s):  
Panca Jarot Santoso ◽  
I Nyoman Pugeg Aryantha ◽  
Sony Suhandono ◽  
Adi Pancoro
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
High Intensity ◽  
Ssr Marker ◽  
Plant Genetics ◽  
Molecular Assays ◽  
Pythium Vexans ◽  
Dna Pools ◽  
Ssr Loci ◽  
Selection Of

<p>Penyakit mati-pohon disebabkan cendawan Pythiaceae khususnya Phytophtora palmivora, Pythium vexans, dan Pythium cucurbitacearum menjadi salah satu kendala utama dalam budidaya durian. Di antara upaya pengendaliannya adalah melalui pemuliaan dan seleksi tanaman tahan berbasis molekuler menggunakan marka SSR. Penelitian untuk mengidentifikasi lokus SSR yang berasosiasi dengan karakter tahan penyakit mati-pohon pada durian telah dilaksanakan di Laboratorium Genetika Tumbuhan SITH-ITB dari bulan April sampai dengan Desember 2014. Penelitian dilaksanakan secara bulked pseudo-segregant analysis dua pool DNA durian tahan dan rentan. Amplifikasi lokus SSR menggunakan 77 pasang primer mikrosatelit berlabel fluorescent. Produk amplifikasi dibaca menggunakan GeneMarker v.2.4.0., setiap puncak pancaran fluorescent yang memiliki nilai intensitas tinggi dipilih sebagai alel. Pembandingan panjang alel dilakukan di antara dua pool dan pembanding aksesi tahan. Lokus yang memiliki alel berbeda antara dua pool tetapi memiliki alel sama dengan pembanding dianggap sebagai marka yang berasosiasi dengan sifat tahan durian terhadap Pythiaceae. Hasil analisis ditemukan tiga lokus mDz03F10, mDz4B2, dan mDz3B1 dengan motif berturut-turut (GAA)3.A(GA)4, (GAGT)2ttGAGT, dan (TTTTATG)2(GCCC)2 teridentifikasi sebagai marka yang berasosiasi dengan karakter tahan Pythiaceae. Hasil analisis ini memerlukan satu langkah validasi untuk meyakinkan keterpautan marka dengan karakter target sebelum digunakan sebagai marka molekuler.</p><p><strong>Keywords</strong></p><p>Durian; SSR; BpSA; Tahan; <em>Pythiaceae</em></p><p><strong>Abstract</strong></p><p>Die-back disease caused by Pythiaceae especially Phytophtora palmivora, Pythium vexans, and Pythium cucurbitacearum is one of the obstacles in durian cultivation. An effort to control this disease is through breeding and selection of resistant plants based on molecular assays such as SSR markers. Research to identify SSR loci associated with durian die-back resistance was done at Plant Genetics Laboratory, SITH-ITB from April to December 2014. The research was conducted through bulked pseudo-segregant analysis of two DNA pools, resistance, and susceptible durians. Amplification of SSR loci was carried out by using 77 fluorescent labeled primers. Amplification products were analyzed using GeneMarker v.2.4.0. Fluorescent peak with high intensity was considered as a selected allele. Comparison of allele length was executed amongst two pools and resistance reference. A locus showed different allele between two pools, while it given the same allele to reference was considered as SSR marker associated with Phytiaceae resistance. The analysis were found three loci, mDz03F10, mDz4B2, and mDz3B1 with motif of (GAA)3.A(GA)4, (GAGT)2ttGAGT, and (TTTTATG)2(GCCC)2 recpectively identified as SSR markers associated to die-back resistance. This result, therefore, requires further validation to convince markers association to target traits before they are used as molecular markers.</p>

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.

Genetic analysis and marker assisted backcrossing for transfer of mosaic virus resistance in cowpea [Vigna unguiculata (L.) Walp.]

2018 ◽  
Author(s):  
H. B. Dinesh ◽  
H. C. Lohithaswa ◽  
K. P. Viswanatha ◽  
L. Manjunatha ◽  
D. S. Ambika ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Ssr Markers ◽  
Bulked Segregant Analysis ◽  
Marker Gene ◽  
Recessive Gene ◽  
Cowpea Mosaic Virus ◽  
Single Marker Analysis ◽  
Transfer Resistance ◽  
Single Marker ◽  
Marker Assisted Backcrossing

Cowpea mosaic virus (CpMV) is known to cause yield loss of as much as 80-100 per cent. Among different approaches available in the management of this disease development and release of resistant varieties is the most viable option for farmers. Hence an investigation was carried out to study the inheritance of resistance to cowpea mosaic virus (CpMV) and to identify DNA markers linked to genomic regions conferring resistance to CpMV. The resistance was found to be governed by single recessive gene in the 191 F2:3 progenies derived from the cross C-152 (susceptible) × V-57817 (resistant). Single marker analysis with 191 F2 individuals and 106 polymorphic SSR markers indicated that two markers, MA15 and MA80 were linked to CpMV resistance as evidenced by significant mean sum of squares due to between marker classes and putative linkage of these markers for resistance to CpMV was confirmed by bulked segregant analysis. Through linkage map constructed utilizing 91 polymorphic SSR markers it was possible for us to show that the two markers MA15 and MA80 were included in the linkage group 6 and the marker gene was likely to be present between these markers. Marker assisted backcrossing was practiced to transfer resistance gene in to an agronomically superior variety C-152.

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