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Genetic Diversity and Molecular Breeding in Plants

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 36172

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Dr. Aakash Chawade

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Department of Plant Breeding, Swedish University of Agricultural Sciences, SE-23053 Alnarp, Sweden
Interests: genetics; plant breeding; bioinformatics; stress
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

It is a paramount task to identify superior germplasms from genebanks and plant breeding programs. Technological advances in various genotyping technologies have made it feasible to genotype a large number of individuals at lower costs, paving the way for large scale studies on plant germplasm characterization. Techniques for transcriptomics, proteomics, and metabolomics are also constantly improving, enabling novel insight into the molecular responses of plants under different conditions.

The Special Issue “Genetic Diversity and Molecular Breeding in Plants” will feature original research articles, literature reviews, and opinion papers on topics including, but not limited to, genetic diversity analysis of germplasm collections, phylogenetic analysis, development of genetic markers, genomic selection, genetic engineering, high-throughput phenotyping, estimation of genetic gain, relative selection efficiency, and new open source software for plant breeding. The Special Issue aims to provide novel insights and new perspectives on accelerating plant breeding in order to develop new cultivars for the changing climate.

Dr. Aakash Chawade
Guest Editor

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Keywords

genetics
genomics
breeding
phenotyping
genetic markers
genomic selection
genetic gain
relative efficiency
genebanks

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Published Papers (9 papers)

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Research

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13 pages, 2095 KiB

Open AccessArticle

Development of Ethyl Methanesulfonate Mutant Edamame Soybean (Glycine max (L.) Merr.) Populations and Forward and Reverse Genetic Screening for Early-Flowering Mutants

by Natsume Koshika, Naohiro Shioya, Takashi Fujimura, Rina Oguchi, Chie Ota, Emi Kato, Reiko Takahashi, Shuichi Kimura, Shinsuke Furuno, Koichi Saito, Kazuhiro Okabe, Masanori Watanabe and Tomoki Hoshino

Plants 2022, 11(14), 1839; https://doi.org/10.3390/plants11141839 - 13 Jul 2022

Cited by 5 | Viewed by 2316

Abstract

Induced mutation is a viable breeding strategy that is widely utilized in the development of elite plant varieties. We aimed to improve a variety of edamame by constructing novel mutant populations using the ethyl methanesulfonate in soybeans (Glycine max (L.) Merr.). In the M₂ population, the flowering stage showed a considerable standard deviation compared to the wild type, confirming that the mutant populations had the expected DNA mutations. To identify the DNA mutations in the mutant populations, we used the targeting induced local lesions in genomes (TILLING) method, which is a reverse genetic method, to search for soybean flowering-related gene mutants. A total of 30 mutants from E1, E3, E4, and PhyA1 genes, which are known to be highly effective genes, or their homologous gene for flowering and maturation found in soybean quantitative trait locus analyses were isolated from our TILLING screening. Among these mutants, there were eleven nonsynonymous substitution mutants, one nonsense mutant, and two single nucleotide deletion mutants that could be expected to reduce or eliminate gene function. The e1, e3, and e4 mutants obtained in this study flowered considerably earlier than the wild type. In particular, the e1 mutant with a nonsynonymous substitution flowered approximately 1 month after sowing regardless of the sowing date, and its harvest date was approximately 1 month earlier than that of the wild type. Mutations identified using the TILLING method could not only be used as gel-based DNA markers with the same manipulation method, but the mutations could also be detected as DNA markers by the high-resolution melting method. These results indicate that mutations achieved without chromosome modification by crossbreeding are effective for early and practical improvement of superior varieties and that efficient selection of mutants by reverse genetics is an effective method for the identification of genetic modifications. The edamame mutant populations developed in this study are believed to possess various useful alleles which may be applicable in the search for mutations that lead to improved edamame yield and eating quality beyond the flowering stage. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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12 pages, 3825 KiB

Open AccessArticle

Genetic Diversity of Rhanterium eppaposum Oliv. Populations in Kuwait as Revealed by GBS

by Fadila Al Salameen, Nazima Habibi, Sami Al Amad and Bashayer Al Doaij

Plants 2022, 11(11), 1435; https://doi.org/10.3390/plants11111435 - 27 May 2022

Cited by 5 | Viewed by 2161

Abstract

Natural populations of Rhanterium eppaposum Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity and population structure. Genotyping by sequencing (GBS) has recently emerged as a powerful tool for the molecular diversity analysis of higher plants without prior knowledge of their genome. This study represents the first effort in using GBS to discover genome-wide single nucleotide polymorphisms (SNPs) of local Rhanterium plants to assess the genetic diversity present in landraces collected from six different locations in Kuwait. The study generated a novel set of 11,231 single nucleotide polymorphisms (SNPs) and indels (insertions and deletions) in 98 genotypes of Rhanterium. The analysis of molecular variance (AMOVA) revealed ~1.5% variation residing among the six populations, ~5% among the individuals within the population and 93% variation present within the populations (F_ST = 0.029; p = 0.0). Bayesian and UPGMA analyses identified two admixed clusters of the tested samples; however, the principal coordinates analysis returned the complete population as a single group. Mantel’s test returned a very weak correlation coefficient of r² = 0.101 (p = 0.00) between the geographic and genetic distance. These findings are useful for the native species to formulate conservation strategies for its sustainable management and desert rehabilitation. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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21 pages, 2925 KiB

Open AccessArticle

Genetic Diversity of Phenotypic and Biochemical Traits in VIR Radish (Raphanus sativus L.) Germplasm Collection

by Anastasia B. Kurina, Dmitry L. Kornyukhin, Alla E. Solovyeva and Anna M. Artemyeva

Plants 2021, 10(9), 1799; https://doi.org/10.3390/plants10091799 - 29 Aug 2021

Cited by 17 | Viewed by 3914

Abstract

Small radish and radish are economically important root crops that represent an integral part of a healthy human diet. The world collection of Raphanus L. root crops, maintained in the VIR genebank, includes 2810 accessions from 75 countries around the world, of which 2800 (1600 small radish, 1200 radish) belong to R. sativus species, three to R. raphanistrum, three to R. landra, and four to R. caudatus. It is necessary to systematically investigate the historical and modern gene pool of root-bearing plants of R. sativus and provide new material for breeding. The material for our research was a set of small radish and radish accessions of various ecological groups and different geographical origin, fully covering the diversity of the species. The small radish subset included 149 accessions from 37 countries, belonging to 13 types of seven varieties of European and Chinese subspecies. The radish subset included 129 accessions from 21 countries, belonging to 18 types of 11 varieties of European, Chinese, and Japanese subspecies. As a result of the evaluation of R. sativus accessions according to phenological, morphological, and biochemical analyses, a wide variation of these characteristics was revealed, which is due to the large genetic diversity of small radish and radish of various ecological and geographical origins. The investigation of the degree of variation regarding phenotypic and biochemical traits revealed adaptive stable and highly variable characteristics of R. sativus accessions. Such insights are crucial for the establishment and further use of trait collections. Trait collections facilitate germplasm use and contribute significantly to the preservation of genetic diversity of the gene pool. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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18 pages, 4260 KiB

Open AccessArticle

Genetic Variation of Native Perilla Germplasms Collected from South Korea Using Simple Sequence Repeat (SSR) Markers and Morphological Characteristics

by Jun Seok Oh, Kyu Jin Sa, Hyeon Park, Do Yoon Hyun, Sookyeong Lee, Ju Hee Rhee and Ju Kyong Lee

Plants 2021, 10(9), 1764; https://doi.org/10.3390/plants10091764 - 25 Aug 2021

Cited by 7 | Viewed by 2844

Abstract

Using morphological characteristics and simple sequence repeat (SSR) markers, we evaluated the morphological variation and genetic diversity of 200 Perilla accessions collected from the five regions of South Korea and another region. In morphological characteristics analysis, particularly leaf color, stem color, degree of pubescence, and leaf size have been found to help distinguish the morphological features of native Perilla accessions cultivated in South Korea. Twenty SSR primer sets confirmed a total of 137 alleles in the 200 Perilla accessions. The number of alleles per locus ranged from 3 to 13, with an average number of alleles per locus of 6.85. The average genetic diversity (GD) was 0.649, with a range of 0.290–0.828. From analysis of SSR markers, accessions from the Jeolla-do and Gyeongsang-do regions showed comparatively high genetic diversity values compared with those from other regions in South Korea. In the unweighted pair group method with arithmetic mean (UPGMA) analysis, the 200 Perilla accessions were found to cluster into three main groups and an outgroup with 42% genetic similarity, and did not show a clear geographic structure from the five regions of South Korea. Therefore, it is believed that landrace Perilla seeds are frequently exchanged by farmers through various routes between the five regions of South Korea. The results of this study are expected to provide interesting information on the conservation of these genetic resources and selection of useful resources for the development of varieties for seeds and leafy vegetables of cultivated Perilla frutescens var. frutescens in South Korea. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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14 pages, 995 KiB

Open AccessArticle

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

by Gunlayarat Bhusudsawang, Ratchanee Rattanawong, Thitaporn Phumichai, Wirulda Pootakham, Sithichoke Tangphatsornruang and Kittipat Ukoskit

Plants 2021, 10(7), 1440; https://doi.org/10.3390/plants10071440 - 14 Jul 2021

Cited by 5 | Viewed by 2666

Abstract

Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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10 pages, 1504 KiB

Open AccessArticle

Fine Mapping of the Gene Controlling the Fruit Skin Hairiness of Prunus persica and Its Uses for MAS in Progenies

by Zhenhua Lu, Lei Pan, Bin Wei, Liang Niu, Guochao Cui, Luwei Wang, Wenfang Zeng and Zhiqiang Wang

Plants 2021, 10(7), 1433; https://doi.org/10.3390/plants10071433 - 14 Jul 2021

Cited by 4 | Viewed by 2370

Abstract

The fruit skin pubescence of Prunus persica is an economically important characteristic and comprises the classification criteria. The mapping and identification of a complete linkage marker to the fruit skin trichome trait locus of peach fruit are critical for the molecular marker-assisted selection for peach/nectarine. In this study, the BC₁ population was constructed from the parents “Zhongyou No. 4”, the recurrent parent, and “Baihuashanbitao”, the non-recurrent parent. Based on the 38 BC₁ individuals’ phenotypes and their genotyping using next-generation sequencing, the G (Glabrous skin) locus of the gene was first identified between 14.099 and 16.721 Mb on chromosome 5. Using other individuals of this population, the gene was fine-mapped in the range of 481 kb with SNP markers. Based on the resequencing data of other cultivars (lines), the candidate SNP in the gene Prupe.5G196400 was obtained. Subsequently, the SNP marker was designed and applied to natural and hybrid peach populations. Via genotyping analysis, we confirmed co-segregation between the peach/nectarine phenotype, which was used in the identification of peach or nectarine with 100% accuracy. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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17 pages, 14996 KiB

Open AccessArticle

Identification of QTLs for Spot Blotch Resistance in Two Bi-Parental Mapping Populations of Wheat

by Navin C. Gahtyari, Chandan Roy, Xinyao He, Krishna K. Roy, Mohamed M. A. Reza, Md. A. Hakim, Paritosh K. Malaker, Arun K. Joshi and Pawan K. Singh

Plants 2021, 10(5), 973; https://doi.org/10.3390/plants10050973 - 13 May 2021

Cited by 8 | Viewed by 3517

Abstract

Spot blotch (SB) disease caused by the hemibiotrophic pathogen Bipolaris sorokiniana inflicting major losses to the wheat grown in warm and highly humid areas of the Indian subcontinent, including Bangladesh, necessitates identification of QTLs stably expressing in Indian subcontinent conditions. Thus, two RIL mapping populations, i.e., WC (WUYA × CIANO T79) and KC (KATH × CIANO T79), were phenotyped at Dinajpur, Bangladesh for three consecutive years (2013-2015) and genotyped on a DArTseq genotyping by sequencing (GBS) platform at CIMMYT, Mexico. In both populations, quantitative inheritance along with transgressive segregation for SB resistance was identified. The identified QTLs were mostly minor and were detected on 10 chromosomes, i.e., 1A, 1B, 2A, 2B, 2D, 4B, 4D, 5A, 5D, and 7B. The phenotypic variation explained by the identified QTLs ranged from 2.3–15.0%, whereby QTLs on 4B (13.7%) and 5D (15.0%) were the largest in effect. The identified QTLs upon stacking showed an additive effect in lowering the SB score in both populations. The probable presence of newly identified Sb4 and durable resistance gene Lr46 in the identified QTL regions indicates the importance of these genes in breeding for SB resistance in Bangladesh and the whole of South Asia. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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22 pages, 3163 KiB

Open AccessArticle

QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population

by Kali M. Brandt, Xianming Chen, Javier F. Tabima, Deven R. See, Kelly J. Vining and Robert S. Zemetra

Plants 2021, 10(3), 572; https://doi.org/10.3390/plants10030572 - 18 Mar 2021

Cited by 9 | Viewed by 3535

Abstract

Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is a worldwide disease of wheat that causes devastating crop losses. Resistant cultivars have been developed over the last 40 years that have significantly reduced the economic impact of the disease on growers, but in heavy infection years it is mostly controlled through the intensive application of fungicides. The Pacific Northwest of the United States has an ideal climate for stripe rust and has one of the most diverse race compositions in the country. This has resulted in many waves of epidemics that have overcome most of the resistance genes traditionally used in elite germplasm. The best way to prevent high yield losses, reduce production costs to growers, and reduce the heavy application of fungicides is to pyramid multiple stripe rust resistance genes into new cultivars. Using genotyping-by-sequencing, we identified 4662 high quality variant positions in a recombinant inbred line population of 196 individuals derived from a cross between Skiles, a highly resistant winter wheat cultivar, and Goetze, a moderately to highly susceptible winter wheat cultivar, both developed at Oregon State University. A subsequent genome wide association study identified two quantitative trait loci (QTL) on chromosomes 3B and 3D within the predicted locations of stripe rust resistance genes. Resistance QTL, when combined together, conferred high levels of stripe rust resistance above the level of Skiles in some locations, indicating that these QTL would be important additions to future breeding efforts of Pacific Northwest winter wheat cultivars. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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Review

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32 pages, 2918 KiB

Open AccessReview

RNA Interference and CRISPR/Cas Gene Editing for Crop Improvement: Paradigm Shift towards Sustainable Agriculture

by Meenakshi Rajput, Khushboo Choudhary, Manish Kumar, V. Vivekanand, Aakash Chawade, Rodomiro Ortiz and Nidhi Pareek

Plants 2021, 10(9), 1914; https://doi.org/10.3390/plants10091914 - 14 Sep 2021

Cited by 26 | Viewed by 10272

Abstract

With the rapid population growth, there is an urgent need for innovative crop improvement approaches to meet the increasing demand for food. Classical crop improvement approaches involve, however, a backbreaking process that cannot equipoise with increasing crop demand. RNA-based approaches i.e., RNAi-mediated gene regulation and the site-specific nuclease-based CRISPR/Cas9 system for gene editing has made advances in the efficient targeted modification in many crops for the higher yield and resistance to diseases and different stresses. In functional genomics, RNA interference (RNAi) is a propitious gene regulatory approach that plays a significant role in crop improvement by permitting the downregulation of gene expression by small molecules of interfering RNA without affecting the expression of other genes. Gene editing technologies viz. the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) have appeared prominently as a powerful tool for precise targeted modification of nearly all crops’ genome sequences to generate variation and accelerate breeding efforts. In this regard, the review highlights the diverse roles and applications of RNAi and CRISPR/Cas9 system as powerful technologies to improve agronomically important plants to enhance crop yields and increase tolerance to environmental stress (biotic or abiotic). Ultimately, these technologies can prove to be important in view of global food security and sustainable agriculture. Full article

(This article belongs to the Special Issue Genetic Diversity and Molecular Breeding in Plants)

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