Genetic diversity of feral alfalfa (Medicago sativa L.) populations occurring in Manitoba, Canada and comparison with alfalfa cultivars: an analysis using SSR markers and phenotypic traits

Agronomic traits such as biomass yield and abiotic stress tolerance are genetically complex and challenging to improve through conventional breeding approaches. Genomic selection (GS) is an alternative approach in which genome-wide markers are used to determine the genomic estimated breeding value (GEBV) of individuals in a population. In alfalfa (Medicago sativa L.), previous results indicated that low to moderate prediction accuracy values (<70%) were obtained in complex traits, such as yield and abiotic stress resistance. There is a need to increase the prediction value in order to employ GS in breeding programs. In this paper we reviewed different statistic models and their applications in polyploid crops, such as alfalfa and potato. Specifically, we used empirical data affiliated with alfalfa yield under salt stress to investigate approaches that use DNA marker importance values derived from machine learning models, and genome-wide association studies (GWAS) of marker-trait association scores based on different GWASpoly models, in weighted GBLUP analyses. This approach increased prediction accuracies from 50% to more than 80% for alfalfa yield under salt stress. Finally, we expended the weighted GBLUP approach to potato and analyzed 13 phenotypic traits and obtained similar results. This is the first report on alfalfa to use variable importance and GWAS-assisted approaches to increase the prediction accuracy of GS, thus helping to select superior alfalfa lines based on their GEBVs.

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Genetic diversity of salt tolerance in tetraploid alfalfa (Medicago sativa L.)

Acta Physiologiae Plantarum ◽

10.1007/s11738-019-2993-8 ◽

2020 ◽

Vol 42 (1) ◽

Cited By ~ 4

Author(s):

Mohamed Ali Benabderrahim ◽

Marwa Guiza ◽

Mansour Haddad

Keyword(s):

Genetic Diversity ◽

Salt Tolerance ◽

Medicago Sativa ◽

Medicago Sativa L

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

Plant Genetic Resources ◽

10.1017/s147926211400063x ◽

2014 ◽

Vol 13 (1) ◽

pp. 56-67

Author(s):

Pawan Khera ◽

Akhilesh Kumar Singh ◽

Rahul Priyadarshi ◽

Durga Khandekar ◽

Rajani K Allu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Hybrid Rice ◽

Fertility Restoration ◽

Phenotypic Traits ◽

Rice Breeding ◽

Coefficient Of Parentage ◽

Rice Germplasm ◽

Cms Line ◽

The Mean

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 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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Analysis of genetic diversity and population structure in Saharan maize (Zea mays L.) populations using phenotypic traits and SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-018-0709-3 ◽

2018 ◽

Vol 66 (1) ◽

pp. 243-257 ◽

Cited By ~ 1

Author(s):

Nawel Belalia ◽

Antonio Lupini ◽

Abderrahmane Djemel ◽

Abdelkader Morsli ◽

Antonio Mauceri ◽

...

Keyword(s):

Genetic Diversity ◽

Zea Mays ◽

Population Structure ◽

Ssr Markers ◽

Zea Mays L ◽

Phenotypic Traits

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Effect of phenotypic recurrent selection on genetic diversity of non-dormant multifoliolate lucerne (Medicago sativa L.) populations

Crop and Pasture Science ◽

10.1071/cp14280 ◽

2015 ◽

Vol 66 (11) ◽

pp. 1190 ◽

Cited By ~ 1

Author(s):

A. Odorizzi ◽

E. M. C. Mamani ◽

P. Sipowicz ◽

B. Julier ◽

J. Gieco ◽

...

Keyword(s):

Genetic Diversity ◽

Medicago Sativa ◽

Recurrent Selection ◽

Selection Process ◽

Phenotypic Recurrent Selection ◽

Total Genetic Diversity ◽

Significant Difference ◽

Medicago Sativa L ◽

Two Populations

The nutritional quality of lucerne (alfalfa, Medicago sativa L.) plants correlates positively with the presence of multifoliolate (MF) leaves. Using phenotypic recurrent selection, we developed populations with an increased percentage of MF expression from 6.7% in the original population (C0) to 77.7% in the fourth cycle (C4). The effect of selection on genetic diversity within and among populations was evaluated. The populations C0 and C4 were represented by 40 plants genotyped by using 25 simple sequence repeats (SSR). The number of alleles per locus was large in both C0 and C4, averaging 6.28. The within-population genetic diversity (HE) overall estimation was 0.723 for C0 and 0.726 for C4, the absence of significant difference between the two populations indicating that the genetic diversity was as large in C4 as in C0. The Nei’s population differentiation (GST) overall estimation was 0.013, meaning that only 1.3% of the total genetic diversity was between populations and 98.7% was within populations. An efficient selection process was conducted without any increase in inbreeding or genetic drift.

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