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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 2021) | Viewed by 17701

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Dr. Nidhi Rawat

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Guest Editor

Plant Science and Landscape Architecture Department, University of Maryland, College Park, MD 20742, USA
Interests: wheat; diseases; genetic resistance; susceptibility; forward and reverse genetics; gene discovery; gene characterization; mechanistic investigations

Special Issue Information

Dear Colleagues,

The world population is expected to reach 8.6 billion by 2030, and 10 billion by 2050, and the need to increase food production is urgent. Furthermore, climate change is manifesting itself as increasing temperature, changing precipitation patterns, increased levels of CO₂ and ozone, increased salinity of agricultural soil, and drought not only affecting crop yields directly, but also reducing the available agricultural land and water. The limited genetic diversity of crops jeopardizes global food security, which is challenged by an increasingly volatile climate and shrinking natural resources. Crops have to be prepared to overcome these challenges and meet the global food supply demand.

Historically, the domestication of crop plants was done by humans by selecting variants for traits controlled by single (or a few) genes such as non-shattering at maturity, apical dominance, easy threshability of cereal grains, and the reduction of acrid compounds in fruits. However, during this selection, a great deal of genetic diversity underlying complex traits such as resistance to disease, heat, and drought stress was lost in the crop plants, creating a “domestication bottleneck” for these crop plants. This limited genetic base was further diminished by the monoculture trend of present times. Wild relatives of crop plants are a rich reservoir of useful genetic diversity for biotic and abiotic stresses. It is crucial to conserve and sustainably utilize these treasure troves of genetic diversity to meet current and future food security demands.

Therefore, in this Special Issue, articles (original research papers, perspectives, hypotheses, opinions, reviews, modeling approaches, and methods) that focus on the genetic resources of crop plants including their discovery; taxonomy; in-situ or ex-situ conservation; cataloging; morphological, physiological, and biochemical evaluation; molecular or sequence-based characterization; and utilization in crops are most welcome.

Dr. Nidhi Rawat
Guest Editor

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Keywords

crop wild relatives
genetic diversity
discovery
taxonomy
conservation
utilization
evaluation
sequencing
cataloging
crop improvement
biotic and abiotic stress tolerance

Published Papers (6 papers)

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Research

10 pages, 1097 KiB

Open AccessFeature PaperArticle

by Magdalena Cieplak, Sylwia Okoń and Krystyna Werwińska

Plants 2021, 10(7), 1424; https://doi.org/10.3390/plants10071424 - 12 Jul 2021

Cited by 7 | Viewed by 2464

Abstract

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation. Full article

(This article belongs to the Special Issue Genetic Resources and Crop Improvement)

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18 pages, 1906 KiB

Open AccessArticle

Mining of Leaf Rust Resistance Genes Content in Egyptian Bread Wheat Collection

by Mohamed A. M. Atia, Eman A. El-Khateeb, Reem M. Abd El-Maksoud, Mohamed A. Abou-Zeid, Arwa Salah and Amal M. E. Abdel-Hamid

Plants 2021, 10(7), 1378; https://doi.org/10.3390/plants10071378 - 05 Jul 2021

Cited by 11 | Viewed by 2618

Abstract

Wheat is a major nutritional cereal crop that has economic and strategic value worldwide. The sustainability of this extraordinary crop is facing critical challenges globally, particularly leaf rust disease, which causes endless problems for wheat farmers and countries and negatively affects humanity’s food security. Developing effective marker-assisted selection programs for leaf rust resistance in wheat mainly depends on the availability of deep mining of resistance genes within the germplasm collections. This is the first study that evaluated the leaf rust resistance of 50 Egyptian wheat varieties at the adult plant stage for two successive seasons and identified the absence/presence of 28 leaf rust resistance (Lr) genes within the studied wheat collection. The field evaluation results indicated that most of these varieties demonstrated high to moderate leaf rust resistance levels except Gemmeiza 1, Gemmeiza 9, Giza162, Giza 163, Giza 164, Giza 165, Sids 1, Sids 2, Sids 3, Sakha 62, Sakha 69, Sohag 3 and Bany Swif 4, which showed fast rusting behavior. On the other hand, out of these 28 Lr genes tested against the wheat collection, 21 Lr genes were successfully identified. Out of 15 Lr genes reported conferring the adult plant resistant or slow rusting behavior in wheat, only five genes (Lr13, Lr22a, Lr34, Lr37, and Lr67) were detected within the Egyptian collection. Remarkedly, the genes Lr13, Lr19, Lr20, Lr22a, Lr28, Lr29, Lr32, Lr34, Lr36, Lr47, and Lr60, were found to be the most predominant Lr genes across the 50 Egyptian wheat varieties. The molecular phylogeny results also inferred the same classification of field evaluation, through grouping genotypes characterized by high to moderate leaf rust resistance in one cluster while being highly susceptible in a separate cluster, with few exceptions. Full article

(This article belongs to the Special Issue Genetic Resources and Crop Improvement)

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12 pages, 3000 KiB

Open AccessEditor’s ChoiceArticle

Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice

by Justine K. Kitony, Hidehiko Sunohara, Mikako Tasaki, Jun-Ichi Mori, Akihisa Shimazu, Vincent P. Reyes, Hideshi Yasui, Yoshiyuki Yamagata, Atsushi Yoshimura, Masanori Yamasaki, Shunsaku Nishiuchi and Kazuyuki Doi

Plants 2021, 10(6), 1255; https://doi.org/10.3390/plants10061255 - 21 Jun 2021

Cited by 22 | Viewed by 3881

Abstract

A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community. Full article

(This article belongs to the Special Issue Genetic Resources and Crop Improvement)

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16 pages, 6625 KiB

Open AccessArticle

Differential Gene Expression Associated with Altered Isoflavone and Fatty Acid Contents in Soybean Mutant Diversity Pool

by Dong-Gun Kim, Jae-Il Lyu, You-Jin Lim, Jung-Min Kim, Nguyen-Ngoc Hung, Seok-Hyun Eom, Sang-Hoon Kim, Jin-Baek Kim, Chang-Hyu Bae and Soon-Jae Kwon

Plants 2021, 10(6), 1037; https://doi.org/10.3390/plants10061037 - 21 May 2021

Cited by 4 | Viewed by 2184

Abstract

Soybean seeds are consumed worldwide owing to their nutritional value and health benefits. In this study we investigated the metabolic properties of 208 soybean mutant diversity pool (MDP) lines by measuring the isoflavone and fatty acid contents of the seed. The total isoflavone content (TIC) ranged from 0.88 mg/g to 7.12 mg/g and averaged 3.08 mg/g. The proportion of oleic acid among total fatty acids (TFA) ranged from 0.38% to 24.66% and averaged 11.02%. Based on the TIC and TFA among the 208 MDP lines, we selected six lines with altered isoflavone content and six lines with altered oleic acid content compared with those of the corresponding wild-types for measuring gene expression. Each of twelve genes from the isoflavone and fatty acid biosynthesis pathways were analyzed at three different seed developmental stages. Isoflavone biosynthetic genes, including CHI1A, IFS1, and IFS2, showed differences in stages and expression patterns among individuals and wild-types, whereas MaT7 showed consistently higher expression levels in three mutants with increased isoflavone content at stage 1. Expression patterns of the 12 fatty acid biosynthetic genes were classifiable into two groups that reflected the developmental stages of the seeds. The results will be useful for functional analysis of the regulatory genes involved in the isoflavone and fatty acid biosynthetic pathways in soybean. Full article

(This article belongs to the Special Issue Genetic Resources and Crop Improvement)

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15 pages, 2695 KiB

Open AccessArticle

Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

by Evangelia Stavridou, Georgios Lagiotis, Parthena Kalaitzidou, Ioannis Grigoriadis, Irini Bosmali, Eleni Tsaliki, Stiliani Tsiotsiou, Apostolos Kalivas, Ioannis Ganopoulos and Panagiotis Madesis

Plants 2021, 10(4), 656; https://doi.org/10.3390/plants10040656 - 30 Mar 2021

Cited by 13 | Viewed by 2808

Abstract

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits. Full article

(This article belongs to the Special Issue Genetic Resources and Crop Improvement)

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13 pages, 1564 KiB

Open AccessArticle

Identification of QTLs for Salt Tolerance at the Germination and Seedling Stages in Rice

by Walid Raafat Nakhla, Wenqiang Sun, Kai Fan, Kang Yang, Chaopu Zhang and Sibin Yu

Plants 2021, 10(3), 428; https://doi.org/10.3390/plants10030428 - 24 Feb 2021

Cited by 20 | Viewed by 2652

Abstract

Rice is highly sensitive to salinity stress during the seedling establishment phase. Salt stress is widely occurring in cultivated areas and severely affects seed germination ability and seedling establishment, which may result in a complete crop failure. The objective of the present study is to identify quantitative trait loci (QTLs) related to salt tolerance of the germination and seedling stages in a rice backcross inbred line (BIL) population that was derived from a backcross of an Africa rice ACC9 as donor and indica cultivar Zhenshan97 (ZS97) as the recurrent parent. Under salt stress, ACC9 exhibited a higher germination percentage, but more repressed seedling growth than ZS97. Using the BIL population, 23 loci for germination parameters were detected at the germination stage and 46 loci were identified for several morphological and physiological parameters at the seedling stage. Among them, nine and 33 loci with the ACC9 alleles increased salt tolerance at the germination and seedling stages, respectively. Moreover, several major QTLs were found to be co-localized in the same or overlapping regions of previously reported genes for salt stress. These major loci will facilitate improving salt-tolerance rice in genome-breeding programs. Full article

(This article belongs to the Special Issue Genetic Resources and Crop Improvement)

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