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Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop...
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Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement

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 (30 April 2024) | Viewed by 12181

Special Issue Editors

Dr. Wenqiang Li

E-Mail Website
Guest Editor
College of Life Sciences, Northwest A&F University, Yangling, China
Interests: rice functional genomics; molecular cell biology; stress tolerance; crops
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Haifeng Li

E-Mail Website
Guest Editor
College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
Interests: wheat; rice; growth and development; functional genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Along with the increased frequency of extreme weather events around the world, including rising temperatures, more intense rainfall and associated flooding, as well as more intense drought in many regions, developing strategies to continue to improve crop yield and quality has become a major challenge. Accelerating crop improvement through the development of new germplasm resources with increased adaptation to adverse environmental factors is still an effective way to increase grain production. Over the last several decades, the success of many breeding programs has been associated with the utilization of the available genetic diversity within elite germplasm. Germplasm resources are a crucial resource to conserve genetic diversity, and can also provide a source of novel traits essential for sustained crop improvement. In this regard, a better understanding of the genetic diversity of new germplasm and gene resources will contribute to the sustained improvement of plants with increased tolerance to adverse environmental conditions.

The forthcoming Special Issue focuses mainly on exploring the genetic diversity and germplasm resources associated with altered tolerance to environmental stresses. There is particular interest in research on the molecular basis of novel alleles and key traits, and their potential biotechnological applications in molecular breeding. The aim of this Special Issue is to provide a better understanding of genetic diversity, germplasm resources, and new biotechnologies for the development of environmental-stress-tolerant plants for sustained crop improvement.

Dr. Wenqiang Li
Prof. Dr. Haifeng Li
Guest Editors

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Keywords

  • genetic diversity
  • germplasm resources
  • biotechnological applications
  • crop improvement
  • genes
  • environmental stress tolerance
  • molecular basis

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Published Papers (6 papers)

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Research

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15 pages, 3210 KiB  
Article
Identifying the Quantitative Trait Locus and Candidate Genes of Traits Related to Milling Quality in Rice via a Genome-Wide Association Study
by Changmin Hu, Xinru Li, Mengyuan Zhang, Chunyu Jing, Mei Hai, Jiaming Shen, Qing Xu, Xiaojing Dang, Yingyao Shi, Erbao Liu and Jianhua Jiang
Plants 2024, 13(10), 1324; https://doi.org/10.3390/plants13101324 - 11 May 2024
Viewed by 885
Abstract
Milling quality directly affects production efficiency in rice, which is closely related to the brown rice recovery (BRR), the milled rice recovery (MRR) and the head milled rice recovery (HMRR). The present study investigated these three traits in 173 germplasms in two environments, [...] Read more.
Milling quality directly affects production efficiency in rice, which is closely related to the brown rice recovery (BRR), the milled rice recovery (MRR) and the head milled rice recovery (HMRR). The present study investigated these three traits in 173 germplasms in two environments, finding abundant phenotypic variation. Three QTLs for BRR, two for MRR, and three for HMRR were identified in a genome-wide association study, five of these were identified in previously reported QTLs and three were newly identified. By combining the linkage disequilibrium (LD) analyses, the candidate gene LOC_Os05g08350 was identified. It had two haplotypes with significant differences and Hap 2 increased the BRR by 4.40%. The results of the qRT-PCR showed that the expression of LOC_Os05g08350 in small-BRR accessions was significantly higher than that in large-BRR accessions at Stages 4–5 of young panicle development, reaching the maximum value at Stage 5. The increase in thickness of the spikelet hulls of the accession carrying LOC_Os05g08350TT occurred due to an increase in the cell width and the cell numbers in cross-sections of spikelet hulls. These results help to further clarify the molecular genetic mechanism of milling-quality-related traits and provide genetic germplasm materials for high-quality breeding in rice. Full article
(This article belongs to the Special Issue Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement)
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16 pages, 3859 KiB  
Article
Characterization of OsPIN2 Mutants Reveal Novel Roles for Reactive Oxygen Species in Modulating Not Only Root Gravitropism but Also Hypoxia Tolerance in Rice Seedlings
by Bowen Hao, Ruihan Zhang, Chengwei Zhang, Na Wen, Yu Xia, Yang Zhao, Qinying Li, Lei Qiao and Wenqiang Li
Plants 2024, 13(4), 476; https://doi.org/10.3390/plants13040476 - 7 Feb 2024
Cited by 1 | Viewed by 1244
Abstract
Tolerance to submergence-induced hypoxia is an important agronomic trait especially for crops in lowland and flooding-affected areas. Although rice (Oryza sativa) is considered a flood-tolerant crop, only limited cultivars display strong tolerance to prolonged submergence and/or hypoxic stress. Therefore, characterization of [...] Read more.
Tolerance to submergence-induced hypoxia is an important agronomic trait especially for crops in lowland and flooding-affected areas. Although rice (Oryza sativa) is considered a flood-tolerant crop, only limited cultivars display strong tolerance to prolonged submergence and/or hypoxic stress. Therefore, characterization of hypoxic resistant genes and/or germplasms have important theoretical and practical significance for rice breeding and sustained improvements. Previous investigations have demonstrated that loss-of-function of OsPIN2, a gene encoding an auxin efflux transporter, results in the loss of root gravitropism due to disrupted auxin transport in the root tip. In this study, we revealed a novel connection between OsPIN2 and reactive oxygen species (ROS) in modulating root gravitropism and hypoxia tolerance in rice. It is shown that the OsPIN2 mutant had decreased accumulation of ROS in root tip, due to the downregulation of glycolate oxidase encoding gene OsGOX6, one of the main H2O2 sources. The morphological defects of root including waved rooting and agravitropism in OsPIN2 mutant may be rescued partly by exogenous application of H2O2. The OsPIN2 mutant exhibited increased resistance to ROS toxicity in roots due to treatment with H2O2. Furthermore, it is shown that the OsPIN2 mutant had increased tolerance to hypoxic stress accompanied by lower ROS accumulation in roots, because the hypoxia stress led to over production of ROS in the roots of the wild type but not in that of OsPIN2 mutant. Accordingly, the anoxic resistance-related gene SUB1B showed differential expression in the root of the WT and OsPIN2 mutant in response to hypoxic conditions. Notably, compared with the wild type, the OsPIN2 mutant displayed a different pattern of auxin distribution in the root under hypoxia stress. It was shown that hypoxia stress caused a significant increase in auxin distribution in the root tip of the WT but not in that of the war1 mutant. In summary, these results suggested that OsPIN2 may play a role in regulating ROS accumulation probably via mediating auxin transport and distribution in the root tip, affecting root gravitropism and hypoxic tolerance in rice seedlings. These findings may contribute to the genetic improvement and identification of potential hypoxic tolerant lines in rice. Full article
(This article belongs to the Special Issue Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement)
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13 pages, 2677 KiB  
Article
The Population Divergence and Genetic Basis of Local Adaptation of Wild Soybean (Glycine soja) in China
by Xiaodong Liu, Peiyuan Li, Xiaoyang Ding, Ying Wang, Guangxun Qi, Jiaxin Yu, Yong Zeng, Dezhi Cai, Xuhang Yang, Jiahui Yang, Chunming Xu, Bao Liu, Yingshan Dong and Na Zhao
Plants 2023, 12(24), 4128; https://doi.org/10.3390/plants12244128 - 11 Dec 2023
Cited by 2 | Viewed by 1491
Abstract
Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. [...] Read more.
Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource. Full article
(This article belongs to the Special Issue Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement)
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21 pages, 5287 KiB  
Article
Genetic Diversity and Population Structure Analyses in Bitter Gourd (Momordica charantia L.) Based on Agro-Morphological and Microsatellite Markers
by K. N. Mallikarjuna, Bhoopal Singh Tomar, Manisha Mangal, Naveen Singh, Deepak Singh, Sachin Kumar, Avinash Tomer, Balraj Singh and Gograj Singh Jat
Plants 2023, 12(19), 3512; https://doi.org/10.3390/plants12193512 - 9 Oct 2023
Cited by 2 | Viewed by 2324
Abstract
Bitter gourd (Momordica charantia L.) is an important vine crop of the Cucurbitaceae family and is well known for its high nutritional and medicinal values. However, the genetic variation remains largely unknown. Herein, 96 diverse bitter gourd genotypes were undertaken for diversity [...] Read more.
Bitter gourd (Momordica charantia L.) is an important vine crop of the Cucurbitaceae family and is well known for its high nutritional and medicinal values. However, the genetic variation remains largely unknown. Herein, 96 diverse bitter gourd genotypes were undertaken for diversity analysis using 10 quantitative traits, and 82 simple sequence repeat (SSR) markers. Out of 82 SSRs, 33 were polymorphic and the mean polymorphism information content (PIC) value was 0.38. Marker, JY-003 revealed a maximum (0.81) PIC value and, the number of alleles per locus ranged from 2 to 7 (average 3.46). The value of gene diversity showed the presence of a significant level of polymorphism among these genotypes. The unweighted pair group method (UPGMA) cluster analysis grouped the genotypes into two major clusters of which Cluster I comprised mostly small and medium-fruited genotypes of both M. charantia var. charantia and M. charantia var. muricata, whereas Cluster II included mostly long and extra-long fruited genotypes. Furthermore, these genotypes were divided into six distinct groups based on population structure analysis. The diversity analysis based on 10 quantitative traits revealed that earliness and high-yielding ability were exhibited by the predominantly gynoecious line DBGS-21-06 followed by DBGS-48-00. The principal component analysis (PCA) revealed that the first two components exhibited more than 50% of the total genetic variation. The present study deciphered a higher magnitude of agro-morphological and genetic diversity in 96 bitter gourd genotypes. Therefore, trait-specific genotypes identified in this study could be utilized in breeding programmes directed towards the development of improved cultivars and hybrids of bitter gourd. Full article
(This article belongs to the Special Issue Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement)
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40 pages, 11212 KiB  
Article
A Comprehensive Genome-Wide Investigation of the Cytochrome 71 (OsCYP71) Gene Family: Revealing the Impact of Promoter and Gene Variants (Ser33Leu) of OsCYP71P6 on Yield-Related Traits in Indica Rice (Oryza sativa L.)
by Bijayalaxmi Sahoo, Itishree Nayak, C. Parameswaran, Mahipal Singh Kesawat, Khirod Kumar Sahoo, H. N. Subudhi, Cayalvizhi Balasubramaniasai, S. R. Prabhukarthikeyan, Jawahar Lal Katara, Sushanta Kumar Dash, Sang-Min Chung, Manzer H. Siddiqui, Saud Alamri and Sanghamitra Samantaray
Plants 2023, 12(17), 3035; https://doi.org/10.3390/plants12173035 - 23 Aug 2023
Cited by 2 | Viewed by 1758
Abstract
The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. [...] Read more.
The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields. Full article
(This article belongs to the Special Issue Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement)
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Review

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23 pages, 402 KiB  
Review
Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding
by Efstathia Lazaridi, Aliki Kapazoglou, Maria Gerakari, Konstantina Kleftogianni, Kondylia Passa, Efi Sarri, Vasileios Papasotiropoulos, Eleni Tani and Penelope J. Bebeli
Plants 2024, 13(6), 758; https://doi.org/10.3390/plants13060758 - 7 Mar 2024
Cited by 6 | Viewed by 3625
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement [...] Read more.
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted. Full article
(This article belongs to the Special Issue Genetic Diversity, Germplasm Resources, and Biotechnological Applications for Sustained Crop Improvement)
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