Bulk segregant analysis identifies SSR markers associated with leaf- and seed-related traits in Perilla crop (Perilla frutescens L.)

2021 ◽  
Author(s):  
Su Eun Lim ◽  
Kyu Jin Sa ◽  
Ju Kyong Lee
Keyword(s):  
Ssr Markers ◽  
Bulk Segregant Analysis ◽  
Perilla Frutescens

Somatic chimerism, genetic inheritance, and mapping of the fleshless berry (flb) mutation in grapevine (Vitis vinifera L.)

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 721-728 ◽  
Author(s):  
L Fernandez ◽  
A Doligez ◽  
G Lopez ◽  
M R Thomas ◽  
A Bouquet ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Bulk Segregant Analysis ◽  
Cell Layer ◽  
Vitis Vinifera L ◽  
Sequence Repeat ◽  
Wild Type ◽  
Target Region ◽  
Simple Sequence

The fleshless berry (flb) mutation of grapevine (Vitis vinifera L. 'Ugni Blanc') impairs the differentiation and division of inner mesocarp cells responsible for flesh in grapevine berries. In order to study the inheritance of the mutation and to map the flb locus, 5 segregating populations were created. Progeny plants were classified as mutant or wild type by scoring for the presence of an ovary phenotype associated with the Flb– phenotype at anthesis. Phenotypic segregation revealed the involvement of a single dominant allele that was heterozygous in the original mutant. Through bulk segregant analysis, microsatellite (simple sequence repeat (SSR)) markers linked to the mutation were identified, and the flb locus was assigned to linkage group 18. The locus position was then refined by analyzing individual progeny and the segregation of SSR markers in the target region with the closest marker 5.6 cM distant from the flb locus. All progeny with the Flb– ovary phenotype differed from the original fleshless berry mutant in that no berries formed after anthesis. Our data suggest that the original mutant plant was a chimera with the mutated allele present in only 1 cell layer (L2 layer) of the ovary and berry.Key words: Vitis vinifera, mutation, genetic mapping, chimerism.

scholarly journals Identification of microsatellite markers linked to thermotolerance in silkworm by bulk segregant analysis and in silico mapping

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 1063-1078 ◽  
Author(s):  
N. Chandrakanth ◽  
S.M. Moorthy ◽  
K.M. Ponnuvel ◽  
V. Sivaprasad
Keyword(s):  
High Temperature ◽  
Ssr Markers ◽  
In Silico ◽  
Bulk Segregant Analysis ◽  
Bulked Segregant Analysis ◽  
Considerable Effect ◽  
Climatic Conditions ◽  
Silk Production ◽  
F2 Population ◽  
High Degree

Silkworm, being a poikilothermic insect, its growth and development is affected by environmental factors especially, temperature. In tropical countries like India, it has considerable effect on silk production due to the prevailing of hot climatic conditions. Previous attempts to evolve silkworm breeds and hybrids tolerant to high temperature by traditional breeding methods have not yielded the desired results. Hence application of new strategies like marker assisted selection (MAS) could be the most effective strategy for developing a thermo-tolerant bivoltine silkworm for sustainable silk production in India. As a prelude, in this study it is aimed to identify simple sequence repeat (SSR) markers closely linked with thermotolerance in silkworm. To do so, 20 silkworm breeds were evaluated at high temperature (36?C) and based on pupation percentage, two multivoltines (Nistari and Cambodge) and two bivoltines (SK4C and BHR3) were identified as thermo-tolerant and one bivoltine (CSR2) was identified as the susceptible breed. These breeds were screened with 85 SSR markers drawn from different linkage groups and out of those, only 11 markers (12.9%) showed distinct polymorphism between thermo-tolerant and susceptible breeds. Further, bulked segregant analysis (BSA) was performed using 11 polymorphic SSR primers, by comparing the SSR profiles of the tolerant (Nistari) and susceptible (CSR2) parents, their F1 and F2 bulks. Nevertheless, only 5 markers generated clear differences in the amplified DNAs between the bulks corresponding to that of the parents suggesting that the DNA regions amplified by these SSR markers are closely linked to thermotolerance in B. mori. The results obtained through bulk segregant analysis was further confirmed by genotyping 5 linked SSR markers using 140 individual F2 progenies. Of these 5 markers, highest Spearman's rho correlation coefficient was shown by S0816 indicating a high degree of closeness between the genotypic and phenotype variations in F2 population. Furthermore, we have also attempted to locate the genes near to S0816 by in silico approach and upshot revealed 3 genes nearer to its sequence on the B. mori genome. The BGIBMGA005249 gene was found to be located nearest to S0816 at a distance of 14.8 Kb. But, further studies are required in this regard to derive a relationship between the thermotolerance and the functional role of identified genes nearer to the closest marker, so that the identified markers can be used to develop a thermo-tolerant silkworm breed through MAS.

Application of SSR Technique for the Identification of Markers Linked to Salinity Tolerance in Rice

2013 ◽  
Vol 19 (2) ◽  
pp. 57-65
Author(s):  
MH Kabir ◽  
MM Islam ◽  
SN Begum ◽  
AC Manidas
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Salinity Tolerance ◽  
Seedling Stage ◽  
Phenotypic Screening ◽  
Salt Tolerant ◽  
Marker Assisted Breeding ◽  
Hydroponic System ◽  
Rice Landrace ◽  
Salt Susceptible

A cross was made between high yielding salt susceptible BINA variety (Binadhan-5) with salt tolerant rice landrace (Harkuch) to identify salt tolerant rice lines. Thirty six F3 rice lines of Binadhan-5 x Harkuch were tested for salinity tolerance at the seedling stage in hydroponic system using nutrient solution. In F3 population, six lines were found as salt tolerant and 10 lines were moderately tolerant based on phenotypic screening at the seedling stage. Twelve SSR markers were used for parental survey and among them three polymorphic SSR markers viz., OSR34, RM443 and RM169 were selected to evaluate 26 F3 rice lines for salt tolerance. With respect to marker OSR34, 15 lines were identified as salt tolerant, 9 lines were susceptible and 2 lines were heterozygous. While RM443 identified 3 tolerant, 14 susceptible and 9 heterozygous rice lines. Eight tolerant, 11 susceptible and 7 heterozygous lines were identified with the marker RM169. Thus the tested markers could be efficiently used for tagging salt tolerant genes in marker-assisted breeding programme.DOI: http://dx.doi.org/10.3329/pa.v19i2.16929 Progress. Agric. 19(2): 57 - 65, 2008

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