Genetic Diversity Analysis of Hedychium Species Based on RAPD and ISSR Markers

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - The present study reports for the first time the genetic diversity assessment of Hedychium species collected...     

Applicability of SCoT and SSR Molecular Markers for Genetic Diversity Analysis in Chrysanthemum morifolium Genotypes

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - Chrysanthemum is ranked second among the most economically important cut flowers after rose. This flower is...     

Use of Molecular and Protein Based Markers for Accessing Genetic Diversity Among Hippophae salicifolia D. Don Genotypes of Uttarakhand

In order to study the genetic diversity among 16 genotypes of Hippophae salicifolia D. Don of Uttarakhand region, random amplified polymorphic DNA (RAPD)–PCR analysis along with protein profiling of seed storage proteins was carried out for selection of superior genotype having high economic importance. A total of 21 RAPD primers were assayed for their specificity in detecting genetic variability in H. salicifolia genotypes, of which 11 RAPD primers were highly reproducible and were found suitable for use in PCR analysis. A total of 198 bands were scored corresponding to an average of 10.8 bands per primer with 138 bands showing polymorphism (73.2 %) with similarity coefficient ranging from 0.011 to 0.999. A dendrogram constructed based on the UPGMA clustering method revealed two major clusters. Cluster-I comprises of 13 cultivars, while cluster-II includes the remaining three cultivars. The cultivar ST-4, ST-5 and ST-16 were quite unique from the remaining cultivars as evident from the dendrogram. The analysis of total seed storage protein (quantitative) and protein profiling (qualitative) among 16 genotypes of H. salicifolia was performed to indentify novel proteins of important functional attributes. SDS-PAGE based generated profiles of seed proteins showed major differences in banding patterns among these genotypes with respect to altitude besides differences in seed protein contents. This study helps in the selection of superior genotype of H. salicifolia having higher economic importance by using developed molecular and protein based markers in Uttarakhand regions.     

Molecular and Phenotypic Characterization of 149 Finger Millet Accessions Using Microsatellite and Agro-Morphological Markers

In the present investigation a diverse range of 149 finger millet accessions representing world collections was characterized using 19 quantitative variables and 46 genomic microsatellite markers. Wide variation was observed for the studied agro-morphological characters between exotic and Indian populations, which consisted of 60 and 89 accessions respectively. The Indian (Asian) accessions were observed to have more flag leaf sheath length, peduncle length, panicle exsertion, ear head width, fingers per head and 1000-grain weight as compared to exotic populations. Highly significant and positive correlations were observed between days to 50 % flowering and days to maturity (0.914); peduncle length and panicle exsertion (0.921). The first three PCA components explained 50 % of the total variation and two major groups were detected on the basis of projection of the accessions on the first two principal components. The genotypes IE7320, IE4491, GE1437, VHC3911, and VHC3898 were found to be better parents for high photosynthetic efficiency, while GE1437, GE5192, and IE5367 were for tryptophan content. The 46 SSR markers grouped 149 genotypes into two groups viz., Indian and exotic, based on the UPGMA analysis of Power Marker V3.25 software. The clustering pattern of Indian and exotic genotypes was similar to some extent on the basis of morphological and molecular markers, however the SSR markers were more effective in explaining the admixture of genotypes. Among the SSRs UGEP65, UGEP24, UGEP60, and UGEP78 are noteworthy due to their relatively higher level of polymorphism which can be widely used for diversity analysis, and QTL mapping studies.     

Genetic Diversity of Genus <Emphasis Type="Italic">Avena</Emphasis> from North Western-Himalayas Using Molecular Markers

The objective of the present study was to estimate the genetic diversity of wild relatives and commercial cultivars of genus Avena, using 22 random amplified polymorphic DNA (RAPD) and 10 simple sequence repeats (SSR) polymorphic markers. These two molecular marker systems were also compared for better genetic characterization of oat species. The patterns of polymorphism revealed by the two marker systems were different and level of polymorphism was higher for SSR (100 %) than RAPD (85.82 %), thus revealing SSR more efficient marker system. UPGMA cluster analysis of both RAPD and SSR data, was used to group 25 genotypes of Avena into two clusters. All commercial cultivars of Avena sativa viz., HJ-6, OS-6, Kent and HFO-114 except PLP-1 were grouped in the same cluster, depicting a narrow genetic base between the commercial cultivars. Clustering differences were also evident between SSR and RAPD derived marker systems, however, both SSR and RAPD markers grouped A. vavilovina, A. abyssinica and A. brevis into the same cluster and were distinguished from other species. Furthermore, hexaploid wild species like A. sterilis (CI 8077), A. byzantina (HFO 60) and tetraploid wild species A. insularis (HFO 865) and diploid A. strigosa (HFO 505) showed genetic divergence from cultivated species, thus may be used in wide hybridization programme for the introgression of desirable traits. The lack of diversity in oat cultivars shown in the present study demonstrates that it is urgent and imperative to enrich the north western-Himalayan oat commercial gene pool by introgression from divergent wild species.     

Genetic Diversity,Population Structure and Correlation Study in Moringa oleifera Lam. Using ISSR and SRAP Markers

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - Moringa oleifera Lam. is promoted in homestead gardens and is extensively cultivated as an affordable...     

Molecular Genetic Diversity of Plectranthus edulis (Vatke) Agnew as Revealed by Inter Simple Sequence Repeat Markers

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - Plectranthus edulis (Vatke) Agnew is an underutilized and neglected ancient Ethiopian indigenous annual tuber...     

Analysis of Genetic Diversity of Indian Tea Accessions Using Two Modified Amplified Fragment Length Polymorphism Methods

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - The authors compared the utility of two variants of Amplified Fragment Length Polymorphism (AFLP) technique,...     

Genetic Diversity and Population Structure of Kenyan Common Bean ( Phaseolus vulgaris L.) Germplasm Using Peroxidase Gene Markers

Common bean (Phaseolus vulgaris L.) is a vital legume used as human food, source of cash income, feed for livestock, and it increases the fertility of soil by its ability to fix nitrogen. The aim of this research was to determine the genetic diversity and population structure of 40 common bean germplasm cultivated in Kenya, using peroxidase gene (POX)-based molecular markers. The loci analyzed showed high diversity and amplified 624 alleles, ranging from 3 to 9 on every locus, with an average of 7.20. The PIC of the POX markers varied from 0.6204 to 0.9110, with an average of 0.7677. The range of the observed heterozygosity was from 0.6667 to 0.9150 with a mean of 0.7945, while the values of the mean genetic diversity ranged from 0.3072 to 0.4425 with a mean of 0.3972. The UPGMA phenogram separated the genotypes into two main genetic clusters, and the genotypes showed no grouping by geographical origins. The highest value of genetic variation was observed between the genotypes obtained from Western, Rift valley and Central regions of Kenya. Population structure analysis grouped the germplasm into 7 gene pools and showed that the genotypes have a common genetic lineage. AMOVA revealed higher genetic diversity (99%) within population than among population (1%), and this offers a reliable base for the design of genetic improvement schemes. Results of the present study can be used in future breeding programs and for the genetic improvement in common bean.     

基于全外显子组测序技术的遗传性血液病分子诊断技术体系

目的 探讨通过全外显子组测序技术建立遗传性血液病的分子诊断技术体系.方法 选择2013年6月至2014年3月于上海交通大学医学院附属上海儿童医学中心就诊的临床表现不典型,但高度怀疑为遗传性血液病的3例患者为研究对象.通过全外显子组测序技术筛选3例患者的候选致病基因的突变位点,并采用基于毛细管电泳技术的Sanger法测序和家系分析对其突变位点进行验证.结果 通过全外显子组测序技术发现了3例患者相应的遗传学损伤,并采用Sanger法对患者及其父母的致病基因位点的测序进行验证,验证结果与患者的遗传学损伤相符,每例患儿均获得了明确的分子诊断结果.结论 在遗传性血液病的分子诊断中,全外显子组测序是候选基因靶向测序的重要补充,且在一定程度上可提高疾病的诊断符合率.     

Foliar Application of Seaweed Sap Enhances Growth,Yield and Quality of Maize in Eastern Himalayas

Maize (Zea mays L.) productivity in hilly regions of North Eastern Region (NER) of India is very low due to limited use of manures and fertilizers. Under such situation, seaweed sap can become an alternative as it is an organic bio-stimulant. Experiment with extracts from marine algae Kappaphycus alvarezii (K sap) and Gracilaria edulis (G sap) was conducted during 2012 and 2013 to assess the efficacy of seaweed saps on growth, productivity and quality of maize and their role in economizing the chemical fertilizer requirement. Results revealed that K or G sap @ 10% and above concentrations along with 100% recommended dose of fertilizer (RDF) recorded significantly higher plant height, dry matter, chlorophyll content, yield attributes and yield of maize compared to control (water spray). The nitrogen (N) and protein content in grain was the highest under 15% K sap + 100% RDF followed by 15% G sap + 100% RDF. Application of K or G sap at 10% concentrations + 100% RDF also significantly increased micronutrient (copper, zinc, manganese and iron) concentrations in maize grains. The available nitrogen, phosphorous and potassium content in soil was recorded to be lowest under 7.5% K sap + 50% RDF. Thus, foliar application of 10% K or G sap along with 100% RDF is recommended for sustainable maize production in NER of India and other ecosystems elsewhere.

     

Morphological and Molecular Characterizations of Guanophilic Fungi of Bats

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - Bats are crucial components of an ecosystem and provide many services such as seed dispersal, pollination,...     

Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology.High-resolution melting (HRM) technology has been widely used to detect specific mutations in DNA.^1,2 Mutations and polymorphisms in DNA amplicons affect the melting profile of DNA duplexes.³ In HRM assays, DNA melting is observed as a sample is warmed over a range of temperatures; duplex melting is visualized as declining fluorescence due to the release of a saturating duplex-dependent fluorescent dye.² In HRM assays, mutation detection usually relies on changes in the temperature at which the peak melting rate is achieved (Tm) or on other features of melting curve shape.⁴ Assays based on HRM of DNA duplexes have been developed to detect mutations associated with cancer⁵ and genetic disease.⁶ HRM technology is also being developed for analysis of specific mutations in bacterial, viral, and parasitic pathogens⁷ that might harbor resistance mutations⁸ or mutations conferring virulence.⁹We developed a rapid assay for measuring nucleic acid diversity that is based on HRM technology.¹⁰ This assay is based on the premise that the magnitude of the temperature range required to melt a particular DNA pool increases with the diversity of molecules in that pool. In the HRM diversity assay, the level of genetic diversity in a pool of DNA amplicons is reported as a single numeric HRM score. This assay has been successfully used to quantify genetic diversity in plasma samples from HIV-infected individuals.^10–12 The results of the assay are highly reproducible^10,13 and are significantly associated with sequence-based diversity measures.¹²HIV diversity may have important clinical, demographic, or subtype-specific correlates. Historically, analysis of HIV diversity has required costly and time-consuming sequencing analysis of individual HIV variants (eg, using cloning, single-genome sequencing, or next-generation sequencing). Although next-generation sequencing is a powerful tool for evaluating HIV diversity, the methods are expensive and require specialized equipment and complex data-handling protocols.^14,15 The HRM diversity assay offers a simple, less expensive, and scalable method for quantifying HIV diversity. HRM scores are associated with HIV disease stage in adults, suggesting that the HRM diversity assay may be useful for cross-sectional analysis of HIV incidence.¹¹ In pediatric populations, the HRM diversity assay has revealed associations between HIV diversity and duration of HIV infection,^13,16 infant survival,¹³ and response to antiretroviral therapy.¹⁶ The HRM diversity assay has also been used to document bottlenecking of viral populations in children exposed to nonsuppressive antiretroviral therapy.¹⁶Previous studies have evaluated the impact of amplicon characteristics and mutation types on Tm. Herein, we characterized the impact of mutation type, amplicon size, mutation location within the amplicon, concentration of mutant DNA in a DNA mixture, and G/C content on HRM score. These data provide a foundation for understanding the output of the HRM diversity assay for analysis of HIV and for other applications.     

Shade Trees Improve Soil Biological and Microbial Diversity in Coffee Based System in Western Ghats of India

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - There are no comprehensive reports available on impact of shaded and un-shaded coffee agrosystems on soil...     

Diversity of Bacillus thuringiensis Isolates Native to Uttarakhand Himalayas,India and Their Bioefficacy Against Selected Insect Pests

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - The huge family status and diversified agricultural applications of Bacillus thuringiesnsis (Bt) Berliner...     

Assessment of Genetic Diversity in Some Indian Lablab purpureus,L. Bean Genotypes Based on RAPD Marker

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - In the present study, ten genotypes of Lablab purpureus L. Sweet bean were screened for genetic divergence by...     

精子凋亡形态分类与分子机制探讨

目的 介绍精子凋亡的形态分类特征,进行分子生物学机制分析,探讨男性不育症的病因.方法 以精液标本进行TUNEL法和瑞-姬染色法,在油镜下观察凋亡精子拍摄图像,确认凋亡精子和介绍两法染色凋亡精子特征.结果 TUNEL法和瑞-姬染色法图像48幅,分别进行形态描述.并进行分子生物学机制探讨.提供凋亡精子的参考范围.结论 睾丸细胞凋亡可发生在支持细胞、生精上皮中的生精细胞,也可以发生在精子的幼稚期和成熟期.为此,在精液中进行精子形态学分类,应检测凋亡精子的比率,对男性不育症鉴别和判断有临床意义.     

Studies on Aluminium Tolerance and Morphological Traits in Rice Lines from North Eastern India

Genetic variation is prerequisite for any crop improvement program as it helps in development of superior recombinants. Forty eight genotypes were evaluated for agronomic traits, yield and characters related to Al tolerance. The components of variability revealed high magnitude and highly heritable nature of the variations. High heritability with high to moderate value of genetic advance over mean was exhibited by majority of morphological traits used in the study. Significant correlations were observed for aluminum tolerance related traits, agronomic and yield traits. Principal components analysis revealed that the first three most informative components accounted for 70 % of the variance. The clustering pattern as revealed by dendrogram, based on average distance, classified the accessions into five clusters. Several high performing genotypes namely, N-861, Khougjai Phou, Posimot, Aaha and Epyo were found in the study which can be used for future breeding purposes.     

Genetic and Molecular Analysis of Wild-Derived Arrhythmic Mice

A new circadian variant was isolated by screening the intercross offspring of wild-caught mice (Mus musculus castaneus). This variant was characterized by an initial maintenance of damped oscillations and subsequent loss of rhythmicity after being transferred from light-dark (LD) cycles to constant darkness (DD). To map the genes responsible for the persistence of rhythmicity (circadian ratio) and the length of free-running period (τ), quantitative trait locus (QTL) analysis was performed using F₂ mice obtained from an F₁ cross between the circadian variant and C57BL/6J mice. As a result, a significant QTL with a main effect for circadian ratio (Arrhythmicity; Arrh-1) was mapped on Chromosome (Chr) 8. For τ, four significant QTLs, Short free-running period (Sfp-1) (Chr 1), Sfp-2 (Chr 6), Sfp-3 (Chr 8), Sfp-4 (Chr 11) were determined. An epistatic interaction was detected between Chr 3 (Arrh-2) and Chr 5 (Arrh-3). An in situ hybridization study of clock genes and mouse Period1::luciferase (mPer1::luc) real-time monitoring analysis in the suprachiasmatic nucleus (SCN) suggested that arrhythmicity in this variant might not be attributed to core circadian mechanisms in the SCN neurons. Our strategy using wild-derived variant mice may provide a novel opportunity to evaluate circadian and its related disorders in human that arise from the interaction between multiple variant genes.     

Identification of RAPD Markers Associated with Morphological, Biochemical and Ionomic Characteristics in Indian Tomato Genotypes

Random Amplified Polymorphic DNA (RAPD) technique is one of the simplest marker techniques used in the differentiation of organisms. In the present study, 28 Indian tomato genotypes along with morphological, biochemical and ionomic characteristics were subjected to RAPD analysis. Ten random primers were selected from 100 operon primers which produced 88 reproducible bands; 89.8 % (79) of bands were polymorphic and 10.2 % (9) were monomorphic. The total number of markers identified by SMA in different parameters were plant height-06, fruit number-07, fruit cluster-03, fruit weight-03, pH-03, titratable acidity-03, TSS-03, total sugars-07, reducing sugars-06, non-reducing sugars-02, and lycopene-05. In case of macroelements, the total number of markers identified in SMA was P-03, K-05, Ca-06, Mg-03; for microelements, Mn-03, Fe-01, Co-06, Ni-06, Cu-04, Bo-06, Na-04, Mo-07, Cd-02 and Li-06. The total markers associated by SMRA showed the following. Plant height-06, fruit number-11, fruit cluster-06, fruit weight-17, pH-03, titratable acidity-04, TSS-04, total sugars-19, reducing sugars-20, non-reducing sugars-14, lycopene-19, P-13, K-18, Ca-03, Mg-03, Iron-13, Co-04, Ni-13, Cu-16, Zn-26, Bo-22, Na-21, Mo-20, Cd-18 and Li-12. The study suggested that the RAPD markers identified could be used in breeding elite tomato genotypes with good characteristics.