scholarly journals DNA Marker Based Diversity Across Rice Genotypes and Advanced Breeding Lines Bred for Temperate India

2022 ◽  
Author(s):  
Nakeeb un Nisa Yetoo ◽  
Aafreen Sakina ◽  
Najeebul Rehman* Sofi ◽  
Asif B. Shikari ◽  
Reyaz R. Mir ◽  
...  
Keyword(s):  
Information Content ◽  
Ssr Markers ◽  
Polymorphism Information Content ◽  
Cooking Quality ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Temperate Japonica ◽  
Breeding Lines ◽  
And Performance

Abstract Background: Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. Methods and results: This study entails the agro-morphological, cooking quality and molecular characterization of 51 genotypes / advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles per locus and an average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. Conclusion: The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing and also the analysis was useful to generate information on indica - japonica classification of our germplasm.

scholarly journals Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1”

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Vivek Kumar Singh ◽  
Brahma Deo Singh ◽  
Amit Kumar ◽  
Sadhna Maurya ◽  
Subbaiyan Gopala Krishnan ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Rice Variety ◽  
Crop Improvement ◽  
Rice Cultivar ◽  
Seedling Stage ◽  
Basmati Rice ◽  
Recurrent Parent ◽  
Foreground Selection

Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.

Rice (Oryza sativa L.) breeding for novel black short grain associated with yield, cooking quality, high nutrition and antioxidant potential derived from indica black rice x japonica white rice

2021 ◽  
Author(s):  
Chanate Malumpong ◽  
Possawat Narumol ◽  
Uthomphon Saichompoo ◽  
Peeranut Tongyos ◽  
Aekchupong Nanta ◽  
...  
Keyword(s):  
Nutritional Value ◽  
Cooking Quality ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Japonica Rice ◽  
Black Rice ◽  
Temperate Japonica ◽  
Breeding Lines ◽  
White Rice ◽  
Pedigree Selection

Abstract The combination of the trend of Japanese food consumption with the health benefits of black rice is in high demand for rice consumers in Thailand. For this challenge, incorporation of desirable traits from temperate japonica white rice, Akitakomachi and tropical indica black rice, Riceberry was performed by pedigree selection with maker assisted selection (MAS) and these desirable traits have been presented in breeding progenies. The three candidate lines showed highly favorable agronomic characteristics and a high grain yield, with short grains and good cooking quality, similar to japonica rice, in a tropical climate. In addition, these lines showed black coloration of the pericarp, indicating high nutritional value (including Fe, Zn, Vit B6, Vit E and folate levels) and phytochemical, antioxidant and antidiabetic activities, similar to those of the Riceberry parent. In terms of the sensory testing of unpolished rice, two breeding lines (69-1-1 and 72-4-3) showed higher scores than their parents. However, only 69-1-1 was identified as japonica type according to its genetic background. Therefore, this breeding program, involving the crossing of a temperate japonica white rice with a tropical indica black rice, can create novel black short grain rice variety adapted to a tropical environment, similar to japonica-type rice.

scholarly journals Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection

2021 ◽  
pp. 1-10
Author(s):  
Karthika Rajendran ◽  
Clarice J. Coyne ◽  
Ping Zheng ◽  
Gopesh Saha ◽  
Dorrie Main ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lens Culinaris ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Phenotypic Data ◽  
Reference Set ◽  
Genome Wide

Abstract Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

scholarly journals Microsatellites in the analysis of wheat genetic diversity

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 1047-1063
Author(s):  
Ankica Kondic-Spika ◽  
Milica Nicic ◽  
Ljiljana Brbaklic ◽  
Dragana Trkulja ◽  
Dragana Miladinovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Ssr Markers ◽  
Microsatellite Loci ◽  
Polymorphism Information Content ◽  
Null Alleles ◽  
Wheat Genotypes ◽  
Rare Alleles ◽  
High Level

Microsatellite markers (SSR) were used to study wheat genetic diversity. A set of 87 wheat genotypes was analysed with four SSR markers. Primers used for the amplification of adequate microsatellite loci (Xgwm) are according to R?DER et al. (2002). Results were obtained using Applied Biosystems 3130 genetic analyser. Total of 28 alleles were determined, i.e. average of 7 alleles per marker. Number of alleles for individual markers ranged from six (Xgwm3) to eight (Xgwm18). The presence of two null alleles for Xgwm18 and Xgwm155 was found. There were five rare alleles (frequency <2%). Polymorphism information content (PIC) values ranged from 0.52 for Xgwm408 to 0.80 for Xgwm18. Mean PIC value was 0.69 for all markers, which signifies a high level of the detected polymorphism. According to the data collected through the analysis of four markers, most genotypes can be grouped in clusters. The results show usefulness of microsatellite markers in detecting polymorphism, identifying genotypes and assessing genetic diversity.

scholarly journals Molecular characterization of rice genotypes for Zinc biosynthetic gene(s) using microsatellite simple sequence repeat (SSR) markers

2015 ◽  
Vol 1 (2) ◽  
pp. 187-197 ◽  
Author(s):  
Md Mukul Mia ◽  
Shanjida Rahman ◽  
Mirza Mofazzal Islam ◽  
Shamsun Nahar Begum ◽  
Lutful Hassan
Keyword(s):  
Information Content ◽  
Ssr Markers ◽  
Polymorphism Information Content ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Polyacrylamide Gel Electrophoresis ◽  
Rice Varieties ◽  
Zn Content ◽  
Rice Genotypes ◽  
Rice Microsatellite

Zinc deficiency is prevalent and affects nearly two billion people in the developing world, where mainly cereals are consumed as staple food by the people. It is essential to study the genetic characters of the rice genotypes containing genes responsible for zinc synthesis so that they can be used as breeding resource to develop nutrient rich rice varieties. In this study, 46 rice (Oryza sativa L., 2n=24) genotypes were studied for their Zinc biosynthesis ability using 3 Rice Microsatellite (RM) markers (RM23, RM217 and RM35) linked to Zn content at Biotechnology Laboratory of Bangladesh Institute of Nuclear Agriculture (BINA) and Genetics and Plant Breeding Laboratory of Bangladesh Agricultural University, Mymensingh during 5 August, 2013 to 30 April, 2014. The DNA samples were isolated by CTAB mini-prep method from 21 days older rice leaf samples followed by Polymerase chain reaction (PCR). Three markers (Rm23, RM35 and RM217) showed effective polymorphism in DNA band appearance for Zn content out of ten SSR markers. The alleles were separated on Polyacrylamide Gel Electrophoresis (PAGE) system. After molecular analyses of DNA bands using Power Marker software, variation was found in allele number, allele frequency, polymorphism information content (PIC) and gene diversity for each genotype. Number of alleles (23, 19 & 13), PIC-polymorphism information content (0.946, 0.911 & 0.829), gene diversity (0.948, 0.917 & 0.846), rare allele (16, 12 & 8) and null allele (0, 16 & 2) were observed for 3 rice microsatellite (RM) markers viz. RM35, RM217 and RM23, respectively for the 46 rice genotypes. A total of 55 alleles were found by using 3 SSR primers for all genotypes. The number of alleles per locus ranged from 13 to 23 with an average of 18.33 out of total 55 alleles. The UPGMA Dendrogram categorized all the varieties into 7 distinct clusters based on 50% of average genetic distance among the 46 genotypes (Figure 2 and Table 7). Since the primers showed almost similar and highest PIC values, based on this study, the larger range of similarity values using SSR markers will provide greater confidence for the assessment of genetic relationships among the varieties. The information obtained from SSR profiling helped in identifying the varieties containing genes for Zn synthesis among the selected rice genotypes. Among all the rice genotypes, Kumra Ghor, Ghigoj, Tilek Kuchi contained high Zn content found in another chemical analysis. Most of the genotypes contained candidate gene for Zn synthesis and can be used as breeding materials to develop nutrient (Zn) rich rice varieties through different selective breeding methods in future.Asian J. Med. Biol. Res. June 2015, 1(2): 187-197

Characterization of new polymorphic functional markers for sugarcane

Genome ◽  
2009 ◽  
Vol 52 (2) ◽  
pp. 191-209 ◽  
Author(s):  
K. M. Oliveira ◽  
L. R. Pinto ◽  
T. G. Marconi ◽  
M. Mollinari ◽  
E. C. Ulian ◽  
...  
Keyword(s):  
Information Content ◽  
Ssr Markers ◽  
Polymorphism Information Content ◽  
Expressed Sequence Tag ◽  
Functional Markers ◽  
Sequence Motifs ◽  
Direct Estimate ◽  
Conserved Sequence ◽  
Expressed Sequence

Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST–SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST–SSR markers were used to screen 18 sugarcane ( Saccharum spp.) varieties. A high proportion (65.5%) of the above EST–SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST–SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST–SSRs were found to be functional, showing homology to known genes. As the EST–SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST–SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity.

Current situation with the core collection of spring triticale of the National Center of Plant Genetic Resources of Ukraine

2018 ◽  
pp. 75-85
Author(s):  
S.V. Chernobai ◽  
V.K. Riabchun ◽  
T.B. Kapustina ◽  
V.S. Melnyk ◽  
O.E. Shchechenko
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Plant Production ◽  
Educational Institutions ◽  
Breeding Lines ◽  
Growing Season Length ◽  
Long Term Storage ◽  
Foreign Countries ◽  
Spring Triticale

Goal. To build up a spring triticale genetic bank to provide breeding, scientific and educational institutions with initial material and to preserve the existing diversity. To update the database of accessions with a set of valuable economic and morphological features. Results and discussion. The methodology and results of the collection formation and evaluation of spring triticale accessions in the National Center for Plant Genetic Resources of Ukraine of Plant Production Institute nd. a V. Ya. Yuriev are presented. The formed collection includes 1,935 accessions from 27 countries: 42 varieties and 1,478 breeding lines from Ukraine, 92 varieties and 248 lines from foreign countries and also 75 genetic lines. The collection was formed by major valuable economic features (plant height, growing season length, spike threshing, yield, 1000-grain weight, disease resistance, technological properties, etc.). Accessions with the majority of morpho-biological and valuable economic features were selected. All the accessions in the collection are certificated. 1,762 accessions were packed for storage into the National Depository; 1,507 of them were packed for long-term storage. Conclusions. The gene pool of spring triticale from the collection of the Gene Bank of Plants of Ukraine is widely used for breeding. This allows conducting hybridization of genetically and ecologically remote forms with various expressions of features and obtaining whole new breeding material. Involvement of collection accessions in breeding allows generating new genetic sources of valuable economic features.

Microsatellite Marker: Importance and Implications of Cross-genome Analysis for Finger Millet (Eleusine coracana (L.) Gaertn)

2020 ◽  
Vol 9 (3) ◽  
pp. 160-170
Author(s):  
Thumadath P.A. Krishna ◽  
Maharajan Theivanayagam ◽  
Gurusunathan V. Roch ◽  
Veeramuthu Duraipandiyan ◽  
Savarimuthu Ignacimuthu
Keyword(s):  
Molecular Marker ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Genome Analysis ◽  
Related Species ◽  
Finger Millet ◽  
Crop Improvement ◽  
Human Beings ◽  
Closely Related Species ◽  
Genome Amplification

Finger millet is a superior staple food for human beings. Microsatellite or Simple Sequence Repeat (SSR) marker is a powerful tool for genetic mapping, diversity analysis and plant breeding. In finger millet, microsatellites show a higher level of polymorphism than other molecular marker systems. The identification and development of microsatellite markers are extremely expensive and time-consuming. Only less than 50% of SSR markers have been developed from microsatellite sequences for finger millet. Therefore, it is important to transfer SSR markers developed for related species/genus to finger millet. Cross-genome transferability is the easiest and cheapest method to develop SSR markers. Many comparative mapping studies using microsatellite markers clearly revealed the presence of synteny within the genomes of closely related species/ genus. Sufficient homology exists among several crop plant genomes in the sequences flanking the SSR loci. Thus, the SSR markers are beneficial to amplify the target regions in the finger millet genome. Many SSR markers were used for the analysis of cross-genome amplification in various plants such as Setaria italica, Pennisetum glaucum, Oryza sativa, Triticum aestivum, Zea mays and Hordeum vulgare. However, there is very little information available about cross-genome amplification of these markers in finger millet. The only limited report is available for the utilization of cross-genome amplified microsatellite markers in genetic analysis, gene mapping and other applications in finger millet. This review highlights the importance and implication of microsatellite markers such as genomic SSR (gSSR) and Expressed Sequence Tag (EST)-SSR in cross-genome analysis in finger millet. Nowadays, crop improvement has been one of the major priority areas of research in agriculture. The genome assisted breeding and genetic engineering plays a very crucial role in enhancing crop productivity. The rapid advance in molecular marker technology is helpful for crop improvement. Therefore, this review will be very helpful to the researchers for understanding the importance and implication of SSR markers in closely related species.

scholarly journals Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

2021 ◽  
Author(s):  
Rajanikanth Govindarajulu ◽  
Ashley N Hostetler ◽  
Yuguo Xiao ◽  
Srinivasa R Chaluvadi ◽  
Margarita Mauro-Herrera ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Interspecific Cross ◽  
Crop Improvement ◽  
Differentially Expressed ◽  
Plant Domestication ◽  
Sorghum Propinquum ◽  
Ril Population ◽  
Trait Locus ◽  
Genomic Regions ◽  
Low Coverage

Abstract Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.

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