Polymorphic SSR Markers Research Articles

Marker-assisted introgression of a major broad spectrum blast resistance gene Pi54 into a popular rice variety Warangal Samba (WGL-14)

Warangal Samba (WGL-14) is a widely known medium slender-grain rice variety that matures within 135-140 days. This variety has been extensively cultivated in Telangana, India, due to its high yield potential of 7-7.5 t/ha and its favourable cooking qualities. However, it is highly susceptible to rice blast disease caused by the fungus Magnaporthe oryzae. This research sought to improve the blast resistance of WGL-14 by incorporating the Pi54 gene, a widely recognized blast resistance gene, using (MABB) along with selection based on phenotypic traits. NLR-145, a high-yielding rice variety containing the Pi54 gene, was used as the donor parent and crossed with WGL-14 to produce F1 plants. The Pi54MAS marker, which is specific to the Pi54 gene, was employed for foreground selection in F1, BC1F1, BC2F1 and BC3F1 generations, while background selection involved 80 parentals polymorphic SSR markers and phenotypic traits observed in each backcross generation. At BC3F5 generation, 28 lines were selected for their strong resistance to blast, high yields, plant type, grain characteristics and other traits comparable to the recurrent parent. These 28 lines were tested in yield trials during the wet seasons from 2018 to 2020 at the Regional Agricultural Research Station (RARS) in Warangal. At Advanced Varietal Trials (AVT), 3 lines namely WGL-1467, WGL-1472 and WGL-1473 were identified as having strong blast resistance and superior agronomic traits, closely resembling the original WGL-14.

Development of Microsatellite Markers from Transcriptome of Eriocheir sinensis and Their Application in Multiplex PCR Panels.

The development of genetic markers is crucial for aquaculture and population genetics. Polyallelic microsatellite markers are widely used for breeding and family management of Eriocheir sinensis (E. sinensis), contributing to the sustainable development of the industry. Through transcriptome analysis, 100 highly polymorphic SSR markers were identified and developed. From these, four multiplex PCR panels, each containing 16 markers, were constructed and applied to parentage assignment in six E. sinensis families. The number of alleles (Na) ranged from 7 to 21, the observed heterozygosity (Ho) varied from 0.356 to 0.951, and the expected heterozygosity (He) varied from 0.656 to 0.909. The polymorphism information content (PIC) ranged from 0.633 to 0.900. The CERVUS analysis showed that using only the two most informative multiplex PCR panels, assignment success rates exceeded 90.34%, with 100% accuracy in assigning offspring to parents when three or four panels were used. This method significantly enhances the efficiency of microsatellite marker analysis, which provides a convenient and cost-effective method for breeding programs and family management of E. sinensis.

Phenotypic, genetic, variation, and molecular function of CaMYB113 in pepper (Capsicum annuum L.).

Pepper (Capsicum annuum L.) is widely consumed vegetables worldwide, and F1 hybrids are highly sought after in the pepper seed industry. However, studies on gene mutations affecting the color of cotyledon are rare, and the same is true for peppers. In this study, a segregating population was developed by crossing the pepper accession 21C1344 with purple cotyledon and accession 21C912 with green cotyledon. Initially, a target genomic region was identified by screening polymorphic SSR markers distributed across 12 chromosomes. Subsequently, polymorphic markers were developed based on resequencing data from the two parental lines, and genetic linkage analysis was performed. This approach ultimately identified Capana10g001433 (CaMYB113) as the candidate gene responsible for the purple cotyledons. The gene mutation type in 21C912 represents a new mutation type distinct from the reported missense mutation types, and this mutation affects the biosynthesis of anthocyanins. Virus-induced gene silencing (VIGS) of CaMYB113 substantially decreased anthocyanin accumulation in the cotyledons. Subsequent overexpression of CaMYB113 resulted in purple callus and leaves of pepper, and changed the expression levels of downstream genes involved in anthocyanin synthesis. Yeast one-hybrid and dual-luciferase transient expression assays demonstrated the binding of CaMYB113 to anthocyanin biosynthesis-related genes, thereby regulating anthocyanin accumulation in pepper cotyledons.

Exploring genetic variation and genetic components under salinity stress among Basmati and Non-Basmati rice (Oryza sativa L.) cultivars

Rice (Oryza sativa L.) is an essential cereal crop which feeds more than half of the world’s population. Rice is cultivated on one-tenth of the world's arable land (approximately 150 million hectares (ha)). Its production is critically affected by salinity stress, which harms photosynthesis and growth, causing biomass loss and partial sterility. The extent of salinization of cultivable soil is increasing by 10% annually. It is predicted that more than 50% of the world's land will be damaged by salinization by 2050. In Pakistan, approximately 6.30 Mha of land is severely affected by salt stress. To cope with this problem, this study was conducted to identify saline-tolerant rice cultivars, 14 rice cultivars (PK1121 aromatic, Nonabokra, Kalomonok, PK10683, PK8892 Tol-19, Shaheen Tol-19, Chenab Tol-19, Punjab Basmati, Super Basmati 2019, Basmati 2000, Basmati 370, Basmati 385, Super Basmati, and Basmati 515 Tol-19) were grown in a 5.5 electrical conductivity (EC) salinity block to investigate their tolerance to salinity stress. Seven rice cultivars (Nonabokra, Basmati 2000, Kalomonok, Basmati 370, Basmati 385, Super Basmati, and Basmati 515 Tol-19) exhibited tolerance to salinity. Basmati 370 was tolerant to a high salinity level of 5.5 EC and showed high yield than other cultivars, however, Nonabokra outperformed other cultivars in terms of all yield attributes investigated in this study. These results were also verified via molecular screening of these genotypes by using already reported DNA markers. Polymorphic SSR marker (RM7075) associated with the SaltTOl QTL to evaluate the tolerance of rice varieties to salinity. This study showed that Nonabokra, Basmati 2000, Kalomonok, Basmati 370, Basmati 385, Super Basmati, and Basmati 515 Tol-19 performed better against salt stress and may be used as salinity-tolerant lines for future rice breeding programs.

The Genetic Diversity of 69 Widely Used Chinese Sorghum Hybrids Released between the 1970s and 2010s

Sorghum has a long history of cultivation in China. In this study, we aimed to clarify the genetic relationships and genetic variation trends in widely used Chinese sorghum hybrids which were released from the 1970s to 2010s and attempted to analyze the changes in sorghum breeding. A total of 257 alleles were detected by 51 polymorphic SSR markers among 69 widely used hybrids; an average of 5.04 alleles were detected by each marker. The average Shannon’s index and polymorphism information content (PIC) of markers were 1.39 and 0.70, respectively. Nei’s genetic diversity index continuously increased in four different breeding development stages (1973–1982, 1983–1992, 1993–2002, and 2003–2014). Genetic diversity gradually increased among the sorghum hybrids. Genetic similarity coefficients in the four breeding development stages first showed an increasing trend, and then a decreasing trend, finally stabilizing with an average value of 0.65. The genetic similarity changes in hybrids in early and late maturing areas were consistent at different breeding development stages. The genetic similarity coefficients in late maturing areas were constantly higher than those in the early maturing areas. This is related to China’s creative utilization of A2 cytoplasmic male sterile materials in the 1990s. A cluster analysis determined that 69 hybrids were divided into two groups, A and B. Group A could be further subdivided into four subgroups. These findings could provide a reference for parental selection and hybrid breeding in sorghum improvement programs.

Genome and transcriptome based comparative analysis of Tilletia indica to decipher the causal genes for pathogenicity of Karnal bunt in wheat

Tilletia indica Mitra causes Karnal bunt (KB) in wheat by pathogenic dikaryophase. The present study is the first to provide the draft genomes of the dikaryon (PSWKBGD-3) and its two monosporidial lines (PSWKBGH-1 and 2) using Illumina and PacBio reads, their annotation and the comparative analyses among the three genomes by extracting polymorphic SSR markers. The trancriptome from infected wheat grains of the susceptible wheat cultivar WL711 at 24 h, 48h, and 7d after inoculation of PSWKBGH-1, 2 and PSWKBGD-3 were also isolated. Further, two transcriptome analyses were performed utilizing T. indica transcriptome to extract dikaryon genes responsible for pathogenesis, and wheat transcriptome to extract wheat genes affected by dikaryon involved in plant-pathogen interaction during progression of KB in wheat. A total of 54, 529, and 87 genes at 24hai, 48hai, and 7dai, respectively were upregulated in dikaryon stage while 21, 35, and 134 genes of T. indica at 24hai, 48hai, and 7dai, respectively, were activated only in dikaryon stage. While, a total of 23, 17, and 52 wheat genes at 24hai, 48hai, and 7dai, respectively were upregulated due to the presence of dikaryon stage only. The results obtained during this study have been compiled in a web resource called TiGeR (http://backlin.cabgrid.res.in/tiger/), which is the first genomic resource for T. indica cataloguing genes, genomic and polymorphic SSRs of the three T. indica lines, wheat and T. indica DEGs as well as wheat genes affected by T. indica dikaryon along with the pathogenecity related proteins of T. indica dikaryon during incidence of KB at different time points. The present study would be helpful to understand the role of dikaryon in plant-pathogen interaction during progression of KB, which would be helpful to manage KB in wheat, and to develop KB-resistant wheat varieties.

Genetic diversity and DNA fingerprinting of rice varieties of Manipur using microsatellite markers

Rice variety differentiation was based on morphological descriptors (DUS) before the advent of genomic and proteomic technology. DNA fingerprinting is becoming an important molecular marker approach because of its wide application in varietal protection, classification, and conflict settlement. In the present study, genetic diversity and variability among the 11 rice varieties of Manipur at the molecular level was studied using 42 SSR markers. The genotypic data of the SSR markers revealed four sub-populations. Cluster analysis indicated the close similarity between RC Maniphou 12 and RC Maniphou 15. To create a DNA fingerprinting database for 11 rice varieties, three separate multiplex PCR systems using different combinations of 11 polymorphic SSR markers based on amplicon size were successfully developed . These were able to distinguish the distinctness of all the eleven released rice varieties.

Multiple cytokinin elevates indirect regeneration potential of indica rice mature embryo

The concept of producing high quality mature seed derived callus competent to genetic transformation followed by efficient full plant regeneration is not unique in rice. But the process is lacking in terms of regeneration efficiency, genotype dependency especially in indica rice. Further, most of the research has only been focused on elite indica cultivars and popular local varieties are neglected. Our extensive literature study also revealed that among all the factors responsible for higher rice regeneration efficiency, the combination, concentration, and type plant growth regulators (PGRs) are mostly responsible for indica rice genotypes. Hence, the present study is focused on standardization of popular local indica rice cultivars for callus induction and regeneration by tweaking the PGRs in culture media, according to their amenability. The plant regeneration potential was assessed on both traditional organogenesis frequency and morphology-based scoring matrix. This revealed the best suitable PGR concentration-combination for efficient organogenesis and the genotype Khitish to be most responsive for indirect regeneration (78.68 ± 1.50 %). The highly polymorphic SSR marker based clonal fidelity test also validated the absence of somaclonal variation among the regenerated plants. This study would be helpful in improving the regeneration potential in local indica rice varieties and genetic transformation studies.

Investigating Genetic Diversity and Population Structure in Rice Breeding from Association Mapping of 116 Accessions Using 64 Polymorphic SSR Markers

Genetic variability in rice breeding programs plays a very crucial role. It provides an outstanding pool of superior alleles governing better agronomic and quality characters through association mapping. For a greater understanding of population structure, the genetic relationship among different rice lines is indispensable prior to the setting of a correlation among dynamic alleles and traits. In the present investigation, the genetic diversity and population structure of 116 rice accessions were studied to understand genetic relatedness and diversity among them using 64 polymorphic SSR markers. A genotyping assessment based on SSR markers revealed a total of 225 alleles, with an average PIC value of 0.755. The germplasm lines were classified into three distinct subgroups through population structure analysis, utilizing both model- and distance-based approaches. AMOVA analysis showed that 11% of the total variation could be attributed to differences between groups, while the remaining 89% was likely due to differences within groups. This study suggested that population structure and genetic relatedness should be considered to establish marker–trait associations for association mapping when working with the core collection of germplasm lines.

Understanding the nature of blast resistance in combined bacterial leaf blight and blast gene pyramided lines of rice variety tellahamsa.

Rice blast and bacterial leaf blight (BLB) are the most limiting factors for rice production in the world which cause yield losses typically ranging from 20 to 30% and can be as high as 50% in some areas of Asia especially India under severe infection conditions. An improved line of Tellahamsa, TH-625-491 having two BLB resistance genes (xa13 and Xa21) and two blast resistance genes (Pi54 and Pi1) with 95% Tellahamsa genome was used in the present study. TH-625-491 was validated for all four target genes and was used for backcrossing with Tellahamsa. Seventeen IBC1F1 plants heterozygous for all four target genes, 19 IBC1F2 plants homozygous for four, three and two gene combinations and 19 IBC1F2:3 plants also homozygous for four, three and two gene combinations were observed. Among seventeen IBC1F1 plants, IBC1F1-62 plant recorded highest recurrent parent genome (97.5%) covering 75 polymorphic markers. Out of the total of 920 IBC1F2 plants screened, 19 homozygous plants were homozygous for four, three and two target genes along with bacterial blight resistance. Background analysis was done in all 19 homozygous IBC1F2 plants possessing BLB resistance (possessing xa13, Xa21, Pi54 and Pi1 in different combinations) with five parental polymorphic SSR markers. IBC1F2-62-515 recovered 98.5% recurrent parent genome. The four, three and two gene pyramided lines of Tellahamsa exhibited varying resistance to blast. Results show that there might be presence of antagonistic effect between bacterial blight and blast resistance genes since the lines with Pi54 and Pi1 combination are showing better resistance than the combinations with both bacterial blight and blast resistance genes.

Molecular and Morphological Profiling of Rice Cultivars Using Hypervariable Microsatellite Markers and DUS Descriptors

Identification and protection of varieties is one of the most important tasks in the plant breeding programme. As the number of new varieties increasing year by year, there is a need to protect and maintain the purity of the varieties. DNA fingerprinting studies allows us to identify the plant varieties with high precision as it is not influenced by environment and other factors. In this context, the present study has been taken up for morphological and molecular profiling of 20 rice genotypes using 39 DUS descriptors and SSR markers. The field experiment was conducted during the year Kharif 2021 and Kharif 2022 at Agricultural Research Station, Bapatla and molecular profiling studies were conducted at RARS, Lam, Guntur. Significant variations were observed for 16 morphological traits at different growth stages, which are relatively more informative in the identification and characterization of rice genotypes. A total of 45 polymorphic SSR markers were used to screen 20 rice genotypes, which produced 336 alleles. The number of alleles produced by these markers ranged from 3 (RM1048) to 15 (RM124) with an average number of alleles of 7.46 per marker. The PIC values of these markers ranged from 0.54 (RM1048) to 0.92 (RM124) with an average PIC value of 0.75. SSR based molecular profiles were developed using 12 highly polymorphic SSR markers viz., RM495, RM6933, RM489, RM6006, RM3351, RM510, RM418, RM3215, RM105, RM6364, RM144 and RM2972 for discrimination of each genotype as well as easy identification.

Development of polymorphic simple sequences repeats markers from whole gene resequencing data comparison of 68 Oncorhynchus mykiss

Rainbow trout (Oncorhynchus mykiss) is a significant cold-water fish farmed in China. Currently, most molecular marker-assisted breeding applications in rainbow trout rely on SSR markers. Although many rainbow trout SSR markers have been developed, methods for mining many polymorphic SSR markers from the genome and identifying them efficiently and rapidly are still lacking. For this reason, this study used in silico simulation method to rapidly develop a large number of polymorphic SSR markers quickly. A total of 354,613 SSR loci with two to six nucleotide repeat motifs were mined from 32 chromosomes of the rainbow trout reference genome using GMATA. The chromosome sequences of the reference genome were then aligned to the whole genome sequencing data (10×) of 68 rainbow trout samples. In silico genotyping was performed using the HipSTR programme to compare and count the variation in the number of repeats of the motifs of the SSR loci in the samples. The loci with high deletion rates and monomorphism were discarded, while those with more than one non-reference allele were kept. The final set of polymorphic SSR loci screened was 78,828. Finally, 4,821 SSR loci were selected with more than 3 alleles and no deletion in all rainbow trout samples and were physically mapped. The average polymorphic information content of these loci was 0.692, indicating high levels of polymorphism. These SSRs were utilized to analyse the genetic diversity and population structure of the 68 rainbow trout samples. The results showed that these 68 samples were divided into two groups. These newly discovered polymorphic SSR markers will provide valuable information for evaluating the construction of rainbow trout family lines for genetic diversity and improvement.

First ever probable oats (Avena sativa) QTLs mapped on chromosome 1 and 7 for pyrenophora leaf spot resistance in India

An experiment was conducted during 2021–22 at Punjab Agricultural University, Ludhiana, Punjab for the development of linkage map and identification of QTLs for pyrenophora or Helminthosporium leaf spot resistance in oats (Avena sativa L.). A total of 96 F2 plants were used which was derived from the cross EC/0007662 (resistant source) and EC/0131291 (susceptible source). Linkage map was constructed for genotypic data of 96 population lines with 24 polymorphic SSR markers using QTL cartographer. A total of 7 linkage groups (LGs) had been generated from this data. But out of 7 LGs, 5 LGs remained individually at 0 position (unlinked) i.e. belonged to different group each and LG1 and LG7 were grouped. First LG included ABAM232, ABAM493 and ABAM077 from 0 to 66.5 cM. Similarly, 7th LG had two marker position i.e. ABAM342 and ABAM425. Maximum distance between the two markers was found to be 33.4 cM (between the marker interval of ABAM232 and ABAM497. Further QTL analysis was done using cartographer with composite interval mapping to identify the QTLs associated with disease resistance by comparing the phenotypic data of F2 population for disease and genotypic data of the population. The work reported here constitutes a major step toward identification of genetic regions responsible for disease resistance. However, the utility of QTL for marker assisted selection requires that QTLs are localized in a narrow region tightly linked with associated markers. The result of the experiment can be used for marker assisted breeding to transfer such genes identified as part of our research in order to reduce disease severity and yield losses in oats.

Assessing the Genetic Diversity of Parents for Developing Hybrids Through Morphological and Molecular Markers in Rice (Oryza sativa L.)

The advancement of hybrid technology plays a crucial role in addressing yield plateau and diminishing resources in rice cultivating regions. The knowledge of genetic diversity among parental lines is a prerequisite for effective hybrid breeding program. In the current study, a set of 66 parental lines was studied for diversity based on both morphological characters and microsatellite SSR markers. The genetic variability parameters unveiled that number of productive tillers per plant, single plant yield and hundred grain weight exhibited additive gene action. Mahalanobis D2 statistics grouped the genotypes into ten clusters based on yield and grain traits. The principal component analysis identified four PCs with eigen value more than one accounting for 71.28% of cumulative variance. The polymorphic SSR markers produced 122 alleles among which the marker RM474 recorded the highest values for Polymorphic Information Content (0.83) and heterozygosity index (0.85). The genotypes were assembled in seven clusters based on jaccard distances using the Unweighted Pair Group method with Arithmetic Mean (UPGMA). The population structure divided the entire population into 3 subpopulations. In both clustering, there was difference in the assembling of genotypes, but, good performing genotypes identified through PCA were positioned in different clusters in both approaches. The genotypes CBSN 495 and CBSN 494 located in different clusters were identified as the potential restorers for high yielding and short duration hybrids. The hybridization among CRR Dhan 310, CRR Dhan 315, IR64 DRT, CB 17135 and WGL 347 can be performed to develop climate smart varieties with improved nutrition.

Unravelling genetic diversity and population structure of Sarocladium oryzae causing sheath rot disease in rice using hyper-variable SSR markers

Rice sheath rot, caused by the fungus Sarocladium oryzae, poses a major threat to rice crops. This pathogen exhibits substantial variability in the field, yet limited information on its genetic diversity and population structure hampers the development of effective disease management strategies. In this study, hyper-variable Simple Sequence Repeats (HV-SSR) markers were employed for the first time to assess the genetic diversity of Sarocladium oryzae, collected from various rice cultivating regions in Odisha, Eastern India. The isolates were identified using both morphological and molecular criteria. A pathogenicity test was performed for all the isolates. A total of 2558 HV-SSRs with more than 10 repeat units were identified in the genome of S. oryzae. The most prevalent types of repeats were dinucleotides (26.8%), followed by trinucleotides (22.8%), tetranucleotides (8.67%), pentanucleotides (2.83%), and hexanucleotides (1.83%). A total of 150 HV-SSR primers were designed and 24 were randomly selected and validated, of which ten of them demonstrating polymorphism in the 87 isolates. These ten polymorphic hyper-variable SSR markers were subsequently used to assess the genetic diversity and population structure of Sarocladium oryzae isolates. The markers revealed a total of 32 alleles, with the number of alleles per locus varying from 2 to 4. Gene diversity ranged from 0.409 to 0.641, while the major allele frequency varied from 0.448 to 0.736. The Polymorphic Information Content (PIC) values ranged from 0.325 to 0.569, with an average of 0.457. Cluster analysis categorized the sheath rot isolates into three distinct major clusters. Principal coordinate analysis and structure analysis identified two genetic clusters within S. oryzae isolates. Analysis of molecular variance indicated that there was more genetic variation within populations (55%) and less variation among populations (45%). The findings of this study provide insights into the genetic diversity of S. oryzae in the rice-cultivating regions of Odisha, which can be used to develop more effective disease management strategies.

Genetic Diversity and Yield Component Analysis in Indian Mustard [Brassica juncea (L.) Czern. and Coss.

Background: Researchers in Indian mustard have made minimal progress in breaking the yield barrier due to limited genetic resources. To increase productivity, a combination of molecular markers and morphological features is advised to boost productivity. The purpose of current work is to characterise polymorphic SSR markers, determine genotype variability, identify suitable parents for hybridization and understand key yield factors. Methods: In 2020-21, twenty-eight Indian mustard varieties and advance breeding materials were evaluated at Ramakrishna Mission Vivekananda Educational and Research Institute’s experimental field in Narendrapur, West Bengal, using statistical techniques to assess genetic estimates and molecular diversity using twenty identified polymorphic SSR primers out of thirty tested primers. Result: The study found that the number of siliqua per plant and primary and secondary branches are crucial yield components determined by correlation and path analysis. The high heritability of ten traits was observed. Genotypes were divided into four clusters with both Mahalanobis’s D2 and molecular diversity analysis, with 1000 seed weight and plant height showing the highest degree of divergence. But the composition of genotypes varied in two types of clusters. Ra1F09 and Ra2B02, SSR markers, showed greater PIC values and heterozygosity among the twenty polymorphic SSR primers. Hybridization between PM25 and high oil content genotypes from cluster I, such as Sanjukta Asech and Kranti, is proposed to produce segregants with high yield, oil content and early maturity.

Morpho-molecular and nutritional profiling for yield improvement and value addition of indigenous aromatic Joha rice of Assam

Short-grain aromatic Joha rice of Assam is a unique class of specialty rice having tremendous potential in domestic and international markets. The poor yielding ability of Assam's Joha rice demands its systematic characterization for an effective breeding program. This study investigates the morphological, molecular and biochemical profiles of twenty popular Joha (aromatic) rice cultivars indigenous to Assam. Distinctiveness, Uniformity and Stability (DUS) characterization of the cultivars revealed polymorphism in thirty-seven traits, establishing distinctiveness for their utilization in breeding programs. Unweighted Neighbor Joining (UNJ) clustering based on usual Euclidean distances for the polymorphic morphological markers grouped the cultivars into three clusters with eight, eleven, and one genotypes. The Joha rice cultivars showed significant differences for all the quantitative traits except for panicle length. The genotypic and phenotypic coefficients of variability (GCV & PCV) were high for grain yield ha−1 (24.62 & 24.85%) and filled grains panicle−1 (23.69 & 25.02%). Mahalanobis D2 analysis revealed three multi-genotypic and four mono-genotypic clusters of the cultivars. The first five principal components explain 85.87% of the variation among the cultivars for the traits under study; filled grain panicle−1 (0.91) and stem thickness (0.55) positively contributed to the first PC. The cultivars' average polyunsaturated fatty acids were 37.9% oleic acid, 39.22% linoleic acid, and 0.5% linolenic acid. Kon Joha 4 and Ronga Joha contained the highest iron (82.88 mg kg−1) and zinc (47.39 mg kg−1), respectively. Kalijeera, Kunkuni Joha, Kon Joha-5, Manimuni Joha and Kon Joha-2 accorded a strong aroma. PCR amplified 174 alleles with a mean value 2.64 across the 66 polymorphic SSR markers. PIC values ranged from 0.091 to 0.698, with an average of 0.326. The highly informative (PIC > 0.50) markers were RM316, RM283, RM585, RM1388, RM3562, RM171, R1M30, RM118, RM11and RM29 for identification of the twenty aromatic rice cultivars. PCR amplification of 27 SSR markers identified 28 unique alleles (97–362 bp) in 13 Joha rice cultivars, which can help their identification/DNA fingerprinting. The UNJ clustering based on Jaccard's coefficients classified the cultivars into three distinct clusters with eight, ten, and two genotypes. Our study revealed the nutritional richness of these specialty Joha rice cultivars and sufficient scope for yield enhancement through their interbreeding to keep quality intact.

Morphological and SSR Marker based Selection for an Elite YMV Resistant Breeding Line from a Segregating Population of Soybean [Glycine max (L.) Merrill

Background: JS335 is a leading variety of soybean in central India with high stability, but YMV susceptible. These leads to the incorporation of the YMV resistance in the elite genotypes of soybean variety JS335. Methods: 45 breeding lines obtained from a cross between two parents SL525 (YMV resistant) and JS335 (YMV susceptible) along with two parents and a check SL958 were analysed for diversity using Mahalanobis D2 and 19 polymorphic SSR markers. These lines were evaluated for yield and component traits and YMV, during 2020 at two locations viz. Ludhiana and Gurdaspur, India. Result: Diversity analysis based on Mahalanobis D2 statistics divided genotypes into five clusters. The maximum (288464.1) and minimum (15103.7) inter-cluster distance were observed between clusters 4 and 5 and clusters 2 and 5, respectively. SSR marker analysis grouped a total of 48 genotypes into three major clusters. The mean for agronomic traits of genotypes was categorised and SLJS 41-2 was found YMV resistant and exhibited a high yield (32.1 g/plant). The contribution of JS 335 towards SLJS 41-2 was found to be 62.5%. This line could further be tested at multilocation to evaluate adaptability and subjected to different yield trials for varietal release or used as a potential YMV donor.

A Novel Set of Chloroplast SSR Markers for the Genus Juglans Reveals Within Species Differentiation

Abstract Juglans is an economically important genus distributed all over the world. Due to its high value, there is a large interest in genetic markers for population genetic analyses and the certification of reproductive material. Using chloroplast genomes of different Juglans species, we developed a highly polymorphic and reliable chloroplast SSR marker set of eleven cpSSRs. It was successfully tested in five different Juglans species. Genetic differentiation among species and provenances within species was assessed. We were able to define a total of nine different chloroplast haplotypes using the novel cpSSR markers with up to four different haplotypes within a single Juglans species. Due to the cost and labor effective character of SSR markers, when compared to other available methods, such as whole chloroplast genome sequencing or SNP analyses, this novel cpSSR marker set will contribute to future population genetic studies in the Juglans genus.

Development of near isogenic lines (NILs) for leaf rust resistance utilizing advanced generation segregating lines of RIL population in wheat (Triticum aestivum L.)

Near-isogenic lines (NILs) are useful genetic resources for basic genetic studies and further understanding of associated molecularmechanisms. The NILs can be developed through standard methods like backcross breeding or advanced generation segregatinglines. The present study aimed the development of NILs for leaf rust resistance from the advanced generation segregating lines withresidual heterozygosity. Advanced generations segregating lines/heterogeneous inbred families (HIFs) segregating for contrastinginfection types (IT ;1 and 3) for leaf rust were identified from the recombinant inbred lines (RILs) between cross of T. timopheevii derivedintrogression line Selection G12, a resistant parent and a susceptible parent Agra local. The molecular analysis using polymorphic SSRmarkers between parents indicated a high level of similarity with 97.07 and 96.49% resemblance among the contrasting NIL pairs fromHIF1 and HIF5, respectively. These NILs may serve as valuable resources for conducting fine mapping and expression analysis of leafrust resistance in wheat and, therefore, will help to identify candidate gene(s) for leaf rust resistance in Selection G12