Genetic variability in trait-specific rice germplasm groups based on coefficient of parentage, SSR markers and fertility restoration

To maximize heterosis, it is important to understand the genetic diversity of germplasm and associate useful phenotypic traits such as fertility restoration for hybrid rice breeding. The objectives of the present study were to characterize genetic diversity within a set of rice germplasm groups using coefficient of parentage (COP) values and 58 simple sequence repeat (SSR) markers for 124 genotypes having different attributes such as resistance/tolerance to various biotic and abiotic stresses. These lines were also used for identifying prospective restorers and maintainers for wild abortive-cytoplasmic male sterile (CMS) line. The mean COP value for all the lines was 0.11, indicating that the genotypes do not share common ancestry. The SSR analysis generated a total of 268 alleles with an average of 4.62 alleles per locus. The mean polymorphism information content value was 0.53, indicating that the markers selected were highly polymorphic. Grouping based on COP analysis revealed three major clusters pertaining to the indica, tropical japonica and japonica lines. A similar grouping pattern with some variation was also observed for the SSR markers. Fertility restoration phenotype based on the test cross of the 124 genotypes with a CMS line helped identify 23 maintainers, 58 restorers and 43 genotypes as either partial maintainers or partial restorers. This study demonstrates that COP analysis along with molecular marker analysis might encourage better organization of germplasm diversity and its use in hybrid rice breeding. Potential restorers identified in the study can be used for breeding high-yielding stress-tolerant medium-duration rice hybrids, while maintainers would prove useful for developing new rice CMS lines.

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Genetic Diversity of Tropical Hybrid Rice Germplasm Measured by Molecular Markers

Rice Science ◽

10.1016/s1672-6308(12)60040-7 ◽

2012 ◽

Vol 19 (3) ◽

pp. 193-201 ◽

Cited By ~ 11

Author(s):

Zhi-zhou HE ◽

Fang-ming XIE ◽

Li-yun CHEN ◽

Madonna Angelita DELA PAZ

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Hybrid Rice ◽

Rice Germplasm

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Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

Genetics Research ◽

10.1017/s0016672307008695 ◽

2007 ◽

Vol 89 (2) ◽

pp. 93-106 ◽

Cited By ~ 37

Author(s):

NOELLE A. BARKLEY ◽

ROB E. DEAN ◽

ROY N. PITTMAN ◽

MING L. WANG ◽

CORLEY C. HOLBROOK ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Data Set ◽

Mini Core Collection ◽

Genomic Ssr ◽

Cultivated Peanut ◽

The Mean ◽

Wild Accessions ◽

Almost All

SummaryThirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15·4 alleles per locus. The mean polymorphic information content (PIC) score was 0·687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10·1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

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Analysis of the polymorphism of expressed sequencetag-Simple sequence repeat in quail

Indian Journal of Animal Research ◽

10.18805/ijar.v0i0f.3803 ◽

2016 ◽

Author(s):

Jun Yan Bai ◽

You Zhi Pang ◽

Yan Xia Qi ◽

Xiao Hui Zhang ◽

Yin Xian Yun

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Improvement ◽

Melanin Synthesis ◽

Sequence Repeat ◽

Average Heterozygosity ◽

Information Contents ◽

The Mean ◽

Simple Sequence

Aiming at accelerating the application of molecular markers in the genetic improvement of quails, six EST-SSR markers were successfully developed using a bioinformatics method. Polymorphisms of three quail populations (Chinese yellow, China black and Korean quail) were detected. The results showed that there were 2-6 alleles in six EST-SSR markers. The mean polymorphism information contents of Chinese yellow , China blackand Korean quail were 0.5451, 0.4962 and 0.4937, respectively. The average heterozygosity values were 0.6134, 0.5759 and 0.5613. Among the six EST-SSR markers, three were highly polymorphicand the others were moderately polymorphic. The newly-developed six EST-SSR markers may be used to determine the genetic diversity of quails. The six EST-SSR markers identified were related to carbohydrate metabolism and melanin synthesis, but the specific mechanisms need to be further analyzed.

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Bioprospecting for fertility restoration genes in wild relatives and land races of rice from different geographic regions

Plant Genetic Resources ◽

10.1017/s1479262117000090 ◽

2017 ◽

Vol 16 (1) ◽

pp. 89-93 ◽

Cited By ~ 1

Author(s):

Amit Kumar Dash ◽

Rashmita Samal ◽

Jwala Narasimha Rao Gundimeda ◽

Hata Nath Subudhi ◽

Nageswara Rao Ravi

Keyword(s):

Hybrid Rice ◽

Fertility Restoration ◽

Wild Relatives ◽

Oryza Rufipogon ◽

Major Advance ◽

Rice Breeding ◽

Line System ◽

Land Races ◽

New Genes ◽

Geographic Regions

AbstractHybrid rice development, a major advance in rice breeding, has demonstrated its immense potential in enhancing the rice productivity. In the three line system of hybrid rice, the restoration of fertility of the widely used wild-abortive type of cytoplasmic male sterility is controlled by Rf3 and Rf4, two fertility restoration genes. Exploration for restorers in diverse genetic backgrounds is a critical step in hybrid rice breeding. As genetic resources constitute the major source of new genes/alleles, an attempt was made to assess the distribution of these two restorer genes in the native populations collected from the geographic regions known to be the primary and secondary centres of origin of rice. In addition, assays were performed on the populations of Oryza rufipogon and Oryza nivara, the wild progenitors of rice. The results suggest that the Rf genes are well distributed in the wild forms at a higher frequency, more in O. rufipogon, while in cultivated forms, their frequency is low, particularly for the Rf3 gene. The genes and the alleles identified in the genetically divergent, low-performing land races and wild relatives can be successfully employed for the development of new hybrid rice cultivars.

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Assessing heat stress tolerance and genetic diversity among exotic and Indian wheat genotypes using simple sequence repeats and agro-physiological traits

Plant Genetic Resources ◽

10.1017/s1479262115000532 ◽

2015 ◽

Vol 15 (3) ◽

pp. 208-220 ◽

Cited By ~ 1

Author(s):

K. T. Ramya ◽

Neelu Jain ◽

Nikita Gandhi ◽

Ajay Arora ◽

P. K. Singh ◽

...

Keyword(s):

Genetic Diversity ◽

Heat Stress ◽

Stress Tolerance ◽

Ssr Markers ◽

Agronomic Traits ◽

Polymorphic Information Content ◽

Group Method ◽

Phenotypic Traits ◽

Heat Stress Tolerance ◽

Simple Sequence

Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.

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Assessment of Genetic Diversity in Rice Germplasm (Oryza sativa L.) using SSR Markers

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2020.905.398 ◽

2020 ◽

Vol 9 (5) ◽

pp. 3346-3355

Author(s):

Akhand Pratap ◽

Prashant Bisen ◽

Bapsila Loitongbam ◽

Sanket R. Rathi ◽

Pragya Parmita ◽

...

Keyword(s):

Genetic Diversity ◽

Oryza Sativa ◽

Ssr Markers ◽

Oryza Sativa L ◽

Rice Germplasm

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Genetic Diversity of Paeonia rockii (Flare Tree Peony) Germplasm Accessions Revealed by Phenotypic Traits, EST-SSR Markers and Chloroplast DNA Sequences

Forests ◽

10.3390/f11060672 ◽

2020 ◽

Vol 11 (6) ◽

pp. 672

Author(s):

Xin Guo ◽

Fangyun Cheng ◽

Yuan Zhong

Keyword(s):

Genetic Diversity ◽

Chloroplast Dna ◽

Ssr Markers ◽

Dna Sequences ◽

Genetic Background ◽

Background Information ◽

Phenotypic Traits ◽

Tree Peony ◽

Chloroplast Dna Sequences ◽

Paeonia Rockii

Research Highlights: This study, based on the first collection of cultivated Paeonia rockii (flare tree peony, FTP) germplasm across the main distribution area by our breeding desires, comprehensively evaluates these accessions by using phenotypic traits, expressed sequence tag (EST)-simple sequence repeat (SSR) markers and chloroplast DNA sequences (cpDNA). The results show that these accessions collected selectively by us can represent the genetic background information of FTP as a germplasm of tree crops. Background and Objectives: FTP has high cultural, ornamental and medicinal value traditionally, as well as recently presenting a significance as an emerging edible oil with high α-linolenic acid contents in the seeds. The objectives of this study are to reveal the characteristics of the genetic diversity of FTP, as well as to provide scientific suggestions for the utilization of tree peony breeding and the conservation of germplasm resource. Materials and Methods: Based on the phenotypic traits, EST-SSR markers and chloroplast DNA sequence variation, we studied the diversity of a newly established population of 282 FTP accessions that were collected and propagated by ourselves in our breeding project in recent years. Results: (1) There was an abundant variation in phenotype of the accessions, and the phenotypic variation was evenly distributed within the population, without significant hierarchical structure, (2) the EST-SSR data showed that these 282 accessions had relatively high genetic diversity, in which a total of 185 alleles were detected in 34 pairs of primers. The 282 accessions were divided into three distinct groups, and (3) the chloroplast DNA sequences (cpDNA) data indicated that these accessions had a higher genetic diversity than the population level and a lower genetic diversity than the species level of wild P. rockii, and the existing spatial genetic structure of these accessions can be divided into two branches. Conclusions: From the results of the three analyses, we found that these accessions can fully reflect the genetic background information of FTP germplasm resources, so their protection and utilization will be of great significance for genetic improvement of woody peonies.

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Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

CABI Agriculture and Bioscience ◽

10.1186/s43170-020-00013-8 ◽

2020 ◽

Vol 1 (1) ◽

Author(s):

G. S. V. Prasad ◽

G. Padmavathi ◽

K. Suneetha ◽

M. S. Madhav ◽

K. Muralidharan

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Crop Improvement ◽

Chromosome 6 ◽

Aromatic Rice ◽

Quality Traits ◽

Combined Analysis ◽

The Core ◽

Rice Germplasm ◽

Core Set

Abstract Background Besides the Basmati, the aromatic rice germplasm (ARG) accessions are treasured for quality, medicinal value and aroma. The demand for aromatic rice is ever increasing. Genetic diversity is the source of variability to identify superior alleles controlling morphological, agronomic and quality traits, and molecular attributes. This study reports on the characterization of traits in ARG to identify a core set for breeding high-yielding varieties. Methods The genetic diversity was measured on the distinctness, uniformity and stability (DUS) of 46 traits in 208 Indian ARG in field, greenhouse and laboratory tests. We performed individual and combined analysis of DUS traits and molecular data generated using 55 SSR markers. The genetic distances between genotypes were estimated using Mahalanobis D2 analysis and clustering by standardized Euclidean2 distances, Ward Minimum variance, Gowers’ similarity index and PowerMarker. The aim was to derive a core set of non-Basmati ARG using PowerCore to deploy in crop improvement. Results Eighty-two alleles were detected. Alleles per marker ranged from 2 (RM505) to 5 (RM276) with an average of 3.04 alleles. The markers are informative in analyzing the diversity as the PIC values estimated varied from 0.17 (RM577 on chromosome 1) to 0.72 (RM276 on chromosome 6) with an average of 0.54 per locus. RM276 with repeat motif of (AG)8A3(GA) 33 on chromosome 6 was the most informative (amplified 5 alleles). The combined analysis had shown genotypes in a few clusters to be more diverse than others. SSR markers RM289, RM505, RM577 and RM22866 were identified as genotype specific markers. With PowerCore, 46 genotypes (22%) were identified as a core set of ARG that represent all the alleles detected in the entire set investigated. 2-Acetyl-1-pyrroline is considered to impart aroma; it was not detected by GC–MS tests in many ARG. Conclusions Forty-six genotypes in the core set have different maturity periods, plant statures, grain types and grain quality traits. A parent can be selected from the core set to improve aromatic rice depending on the breeding objective. The olfactory sensing of strong aroma emitted by cooked kernels of all ARG was found more decisive than the costly GC–MS tests.

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Exploring the Genetic Diversity of Some Squash (Cucurbita Maxima L.) Germplasm Using Morphological and Molecular Markers in Erzincan

10.21203/rs.3.rs-848708/v1 ◽

2021 ◽

Author(s):

HALIL IBRAHIM OZTURK ◽

Veysel Dönderalp ◽

Hüseyin Bulut ◽

Recep Korkut ◽

Arash HOSSEINPOUR ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Ssr Markers ◽

Molecular Level ◽

Polymorphic Information Content ◽

Plant Genetic Resources ◽

Molecular Characteristics ◽

Cucurbita Maxima ◽

High Genetic Diversity ◽

The Mean

Abstract Background Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. Cucurbita maxima species in the cucurbitaceae family have high genetic diversity, but its genetic diversity at the molecular level is inadequately characterized. Methods and Results To determine the genetic diversity among genotypes of Cucurbita maxima species of squash, which is widely grown in Erzincan, 14 different squash genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple sequence repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. Seven SSR markers yielded a total of 23 polymorphic bands, the number of alleles per marker ranged from 2 to 5, and the mean number of alleles was 3.286. Polymorphic information content (PIC) ranged from 0.00 (GMT-M61) to 0.202 (GMT-P25), and the mean PIC value per marker was 0.130. Cluster analysis using Nei's genetic distance determined that 14 genotypes were divided into 3 major groups. Conclusions The SSR markers used were effective in distinguish among similar winter squash or pumpkin and therefore can be beneficial for consideration of Cucurbita maxima species diversity, screening of genetic resources and their selection.

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