scholarly journals Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to WaterStressed Environments

Agronomy ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 487 ◽  
Author(s):  
Acuña ◽  
Rivas ◽  
Brambilla ◽  
Cerrillo ◽  
Frusso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Stress Resistance ◽  
Prunus Persica ◽  
Agronomic Traits ◽  
Phenotypic Traits ◽  
Flesh Color ◽  
Japanese Plum ◽  
Prunus Salicina

The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

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

2015 ◽  
Vol 15 (3) ◽  
pp. 208-220 ◽  
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.

scholarly journals Functional Markers for Precision Plant Breeding

2020 ◽  
Vol 21 (13) ◽  
pp. 4792
Author(s):  
Romesh K. Salgotra ◽  
C. Neal Stewart
Keyword(s):  
Abiotic Stress ◽  
Plant Breeding ◽  
Stress Resistance ◽  
High Throughput Sequencing ◽  
Agronomic Traits ◽  
Direct Selection ◽  
Phenotypic Traits ◽  
Functional Markers ◽  
Grand Challenge ◽  
Biotic And Abiotic Stress

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.

scholarly journals Genetic characterization of Japanese plum cultivars (Prunus salicina) using SSR and ISSR molecular markers

2012 ◽  
Vol 39 (3) ◽  
pp. 533-543 ◽  
Author(s):  
Basilio Carrasco ◽  
Carole Díaz ◽  
Mario Moya ◽  
Marlene Gebauer ◽  
Rolando García-González
Keyword(s):  
Molecular Markers ◽  
Genetic Characterization ◽  
Japanese Plum ◽  
Prunus Salicina ◽  
Issr Molecular Markers

scholarly journals Silencing of one copy of the translation initiation factor eIFiso4G in Japanese plum (Prunus salicina) impacts susceptibility to Plum pox virus (PPV) and small RNA production

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Julia Rubio ◽  
Evelyn Sánchez ◽  
David Tricon ◽  
Christian Montes ◽  
Jean-Philippe Eyquard ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Prunus Persica ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Plum Pox Virus ◽  
Loss Of Function ◽  
Initiation Complex ◽  
Crop Species ◽  
Japanese Plum ◽  
Prunus Salicina

Abstract Background In plants, host factors encoded by susceptibility (S) genes are indispensable for viral infection. Resistance is achieved through the impairment or the absence of those susceptibility factors. Many S genes have been cloned from model and crop species and a majority of them are coding for members of the eukaryotic translation initiation complex, mainly eIF4E, eIF4G and their isoforms. The aim of this study was to investigate the role of those translation initiation factors in susceptibility of stone fruit species to sharka, a viral disease due to Plum pox virus (PPV). Results For this purpose, hairpin-inducing silencing constructs based on Prunus persica orthologs were used to generate Prunus salicina (Japanese plum) 4E and 4G silenced plants by Agrobacterium tumefaciens-mediated transformation and challenged with PPV. While down-regulated eIFiso4E transgenic Japanese plums were not regenerated in our conditions, eIFiso4G11-, but not the eIFiso4G10-, silenced plants displayed durable and stable resistance to PPV. We also investigated the alteration of the si- and mi-RNA profiles in transgenic and wild-type Japanese plums upon PPV infection and confirmed that the newly generated small interfering (si) RNAs, which are derived from the engineered inverted repeat construct, are the major contributor of resistance to sharka. Conclusions Our results indicate that S gene function of the translation initiation complex isoform is conserved in Prunus species. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of the different isoforms of proteins involved in this complex to breed for resistance to sharka in fruit trees.

scholarly journals Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259883
Author(s):  
Seltene Abady ◽  
Hussein Shimelis ◽  
Pasupuleti Janila ◽  
Shasidhar Yaduru ◽  
Admire I. T. Shayanowako ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Drought Tolerance ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Environment Interaction ◽  
Optimum Conditions ◽  
Pod Yield ◽  
Germplasm Collections

Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons. Ninety-nine of the test genotypes were profiled with 16363 SNP markers. Pod yield per plant (PY), seed yield per plant (SY), and harvest index (HI) were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes ICGV 07222, ICGV 06040, ICGV 01260, ICGV 15083, ICGV 10143, ICGV 03042, ICGV 06039, ICGV 14001, ICGV 11380, and ICGV 13200 ranked top in terms of pod yield under both drought-stressed and optimum conditions. PY exhibited a significant (p ≤ 0.05) correlation with SY, HI, and total biomass (TBM) under both test conditions. Based on the principal component (PC) analysis, PY, SY, HSW, shelling percentage (SHP), and HI were allocated in PC 1 and contributed to the maximum variability for yield under the two water regimes. Hence, selecting these traits could be successful for screening groundnut genotypes under drought-stressed and optimum conditions. The model-based population structure analysis grouped the studied genotypes into three sub-populations. Dendrogram for phenotypic and genotypic also grouped the studied 99 genotypes into three heterogeneous clusters. Analysis of molecular variance revealed that 98% of the total genetic variation was attributed to individuals, while only 2% of the total variance was due to variation among the subspecies. The genetic distance between the Spanish bunch and Virginia bunch types ranged from 0.11 to 0.52. The genotypes ICGV 13189, ICGV 95111, ICGV 14421, and ICGV 171007 were selected for further breeding based on their wide genetic divergence. Data presented in this study will guide groundnut cultivar development emphasizing economic traits and adaptation to water-limited agro-ecologies, including in Ethiopia.

scholarly journals Genetic Diversity among Lathyrus ssp. Based on Agronomic Traits and Molecular Markers

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1182 ◽  
Author(s):  
Meriem Miyassa Aci ◽  
Antonio Lupini ◽  
Giuseppe Badagliacca ◽  
Antonio Mauceri ◽  
Emilio Lo Presti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Protein Content ◽  
Structure Analysis ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

Grasspea (Lathyrus sativus L.) and its relatives are considered resilient legumes due to their high ability to cope with different stresses. In this study, the genetic diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was assessed by agronomic traits and molecular markers (Simple Sequence Repeat-SSR) in order to detect accessions useful for future breeding strategies. Phenotypic traits showed a high significant variation in which 1000 seed weight (1000 SW) and protein content appeared the most discriminant, as observed by principal component analysis (PCA). SSR analysis was able to detect forty-eight different alleles with an average of 9.6 allele per locus, and a Polymorphic Information Content (PIC) and a gene diversity of 0.745 and 0.784, respectively. Cluster analysis based on agronomic traits as well as molecular data grouped accessions by species but not by geographical origin. This result was confirmed by Principal Coordinates Analysis (PCoA) and Structure Analysis as well. Moreover, genetic structure analysis revealed a high genetic differentiation between L. ochrus and the other species. Analysis of MOlecular Variance (AMOVA) displayed a greater genetic diversity within species (77%) than among them (23%). Finally, a significant positive correlation was observed between agronomic and genetic distances (Mantel’s test). In conclusion, the variability detected within accessions in each species and the differences among species may be useful to plan next breeding programs, focusing on biomass production as well as protein content.

scholarly journals Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1748
Author(s):  
Brenda I. Guerrero ◽  
M. Engracia Guerra ◽  
Sara Herrera ◽  
Patricia Irisarri ◽  
Ana Pina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Group Method ◽  
Japanese Plum ◽  
Pair Group ◽  
Prunus Salicina ◽  
Wide Range ◽  
High Level ◽  
Informative Content

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

scholarly journals Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Litang Lu ◽  
Hufang Chen ◽  
Xiaojing Wang ◽  
Yichen Zhao ◽  
Xinzhuan Yao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Agronomic Traits ◽  
Association Studies ◽  
Functional Characterization ◽  
Principal Component ◽  
Tea Plant ◽  
Guizhou Province ◽  
Genome Wide Association Studies ◽  
Tea Plants

AbstractThe ancient tea plant, as a precious natural resource and source of tea plant genetic diversity, is of great value for studying the evolutionary mechanism, diversification, and domestication of plants. The overall genetic diversity among ancient tea plants and the genetic changes that occurred during natural selection remain poorly understood. Here, we report the genome resequencing of eight different groups consisting of 120 ancient tea plants: six groups from Guizhou Province and two groups from Yunnan Province. Based on the 8,082,370 identified high-quality SNPs, we constructed phylogenetic relationships, assessed population structure, and performed genome-wide association studies (GWAS). Our phylogenetic analysis showed that the 120 ancient tea plants were mainly clustered into three groups and five single branches, which is consistent with the results of principal component analysis (PCA). Ancient tea plants were further divided into seven subpopulations based on genetic structure analysis. Moreover, it was found that the variation in ancient tea plants was not reduced by pressure from the external natural environment or artificial breeding (nonsynonymous/synonymous = 1.05). By integrating GWAS, selection signals, and gene function prediction, four candidate genes were significantly associated with three leaf traits, and two candidate genes were significantly associated with plant type. These candidate genes can be used for further functional characterization and genetic improvement of tea plants.

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