Pre-breeding towards the Effective Utilization of Plant Genetic Resources Volume II

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 (20 October 2022) | Viewed by 19744

Special Issue Editors


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Guest Editor
Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
Interests: genetic resource development; wide hybridization; molecular breeding; domestication genetics
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Associate Dean, Agricultural College, Hyderabad 500030, Telangana, India
Interests: molecular genetics; QTL mapping; molecular breeeding; bioinformatics

Special Issue Information

Dear Colleagues,

There are approximately 300,000 plants species on Earth, but only 15 provide 90% of food for human consumption. In the face of continuous agro-environmental decline brought about by climate change, strategies that can maximize the utilization of plant genetic resources will be critical in our collective efforts to develop crops with improved adaptation to temperature extremes, drought, flooding, and saline soils, as well as to new biotypes of pests and diseases.

Extensive germplasm collections that include popular cultivars, landraces, and wild relatives of grain, fruit, and vegetable crops have been established in thousands of genebanks worldwide. In spite of this, utilization of plant genetic resources remains low because of various factors, including the lack of information regarding traits of interest in the germplasm, preference of breeders for working collections, and the challenges associated with the direct use of plant genetic resources in breeding (i.e., reproductive incompatibility and linkage drags).

Pre-breeding is the first key step in utilizing the genetic diversity present in germplasm collections. It encompasses activities designed to identify agronomic traits and/or genes of interest from unadapted plant materials that cannot be used directly in breeding and introgressing them into an intermediate form of materials that breeders can readily be used to produce improved crop varieties.

This Special Issue on “Pre-Breeding Toward Effective Utilization of Plant Genetic Resources” includes papers on both basic and applied research highlighting all aspects of pre-breeding activities, from the evaluation of plant genetic resources to identify donors for desirable agronomic traits to the transfer of these target traits into well-adapted genetic backgrounds by hybridizations to generate populations that can be used for actual breeding programs.

Dr. Rosalyn B. Angeles-Shim
Dr. Balram Marathi
Guest Editor

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Keywords

  • plant genetic resources
  • wild crop relatives
  • genetic variation
  • crop improvement
  • climate change
  • adaptation
  • germplasm
  • wide hybridization
  • introgression lines

Published Papers (8 papers)

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Research

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20 pages, 4958 KiB  
Article
Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species
by Aldrin Y. Cantila, William J. W. Thomas, Philipp E. Bayer, David Edwards and Jacqueline Batley
Plants 2022, 11(22), 3010; https://doi.org/10.3390/plants11223010 - 8 Nov 2022
Cited by 2 | Viewed by 2347
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 [...] Read more.
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars. Full article
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12 pages, 238 KiB  
Article
The Use of Pathotype Data for the Selection and Development of Barley Lines with Useful Resistance to Scald
by Hugh Wallwork, Mark Butt, Milica Grcic and Tara Garrard
Plants 2022, 11(19), 2501; https://doi.org/10.3390/plants11192501 - 24 Sep 2022
Cited by 2 | Viewed by 1156
Abstract
Resistance in barley to scald caused by Rhynchosporium commune is readily overcome as virulent pathotypes in the pathogen population are selectively favoured over less virulent pathotypes. Diverse sources of resistance amongst host accessions have been found upon screening a wide array of accessions [...] Read more.
Resistance in barley to scald caused by Rhynchosporium commune is readily overcome as virulent pathotypes in the pathogen population are selectively favoured over less virulent pathotypes. Diverse sources of resistance amongst host accessions have been found upon screening a wide array of accessions from around the world. Deciding which of these is of greatest value, and which are different from each other, takes a much greater investment of time and effort. This paper reports on the use of seedling screening techniques using 262 individual scald isolates collected from around Australia, to identify the most useful resistance sources from amongst 30 previously selected. No resistance source was effective against all isolates, but some such as Pamunkey, CI8618, CI4364 and ICARDA 4 were shown to have resistance to most isolates, whilst others were much less useful. Some of the most effective donors were shown to likely have more than one gene involved. The value of gene pyramids is discussed, as are the advantages and pitfalls of transferring the resistances from poorly adapted genetic backgrounds into better-adapted breeding lines so that they can more readily be used by breeding programs. This is a work in progress and the introgressed resistances being developed are available to all. Full article
15 pages, 3408 KiB  
Article
Targeted Metabolomics Provide Chemotaxonomic Insights of Medicago ruthenica, with Coupled Transcriptomics Elucidating the Mechanism Underlying Floral Coloration
by Lin Zhu, Hongyan Li, Zinian Wu, Zhiyong Li, Maowei Guo, Bu Ning, Wanpeng Liu, Qian Liu, Lei Liu, Zhiyong Wang, Jun Li and Fugui Mi
Plants 2022, 11(18), 2408; https://doi.org/10.3390/plants11182408 - 15 Sep 2022
Cited by 1 | Viewed by 1707
Abstract
Medicago ruthenica, a wild legume forage widely distributed in the Eurasian steppe, demonstrates high genetic and phenotypic variation. M. ruthenica with a purely yellow flower (YFM), differing from the general phenotype of M. ruthenica with a purple flower (PFM), was recently discovered. [...] Read more.
Medicago ruthenica, a wild legume forage widely distributed in the Eurasian steppe, demonstrates high genetic and phenotypic variation. M. ruthenica with a purely yellow flower (YFM), differing from the general phenotype of M. ruthenica with a purple flower (PFM), was recently discovered. The similar characteristics of YFM with Medicago falcata have led to conflicting opinions on its taxonomy using traditional morphological methods. The lack of chemotaxonomy information about M. ruthenica species and the unclear flower coloration mechanisms have hampered their study. Here, we investigated M. ruthenica using targeted metabolomics based on the chemotaxonomy method and elaborated the floral coloration mechanisms using transcriptomics. The identified flavonoids were the same types, but there were different contents in YFM and PFM, especially the contents of cyanidin-3-O-glucoside (C3G), an anthocyanin that causes the purple-reddish color of flowers. The over-accumulation of C3G in PFM was 1,770 times more than YFM. Nineteen anthocyanin-related genes were downregulated in YFM compared with their expression in PFM. Thus, YFM could be defined as a variety of M. ruthenica rather than a different species. The loss of purple flower coloration in YFM was attributed to the downregulation of these genes, resulting in reduced C3G accumulation. The taxonomic characteristics and molecular and physiological characteristics of this species will contribute to further research on other species with similar external morphologies. Full article
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9 pages, 249 KiB  
Article
Use of Botanical Varieties of Brassica oleracea L. in the Breeding of Forage Kale
by John E. Bradshaw
Plants 2022, 11(16), 2160; https://doi.org/10.3390/plants11162160 - 20 Aug 2022
Cited by 1 | Viewed by 1455
Abstract
At present, forage kale cultivars for feeding cattle and sheep are either open-pollinated ones from population-improvement schemes within suitable botanical varieties of Brassica oleracea or triple-cross hybrids from within or between botanical varieties, the only commercialised latter type being between marrow-stem kale and [...] Read more.
At present, forage kale cultivars for feeding cattle and sheep are either open-pollinated ones from population-improvement schemes within suitable botanical varieties of Brassica oleracea or triple-cross hybrids from within or between botanical varieties, the only commercialised latter type being between marrow-stem kale and Brussels sprouts. Eight botanical varieties (15 cultivars) and 13 types of hybrids (50 hybrids) between them were produced and assessed for forage traits in SE Scotland in the early 1980s when there was government funding in Great Britain for such work (terminated in 1990). These previously unpublished results may now be of interest to a new generation of commercial forage brassica breeders. In addition to height and dry matter yield and content, quality traits, such as digestibility and antimetabolites, were assessed. The hybrids with marrow-stem kale as one parent varied in height, but combined a high-dry-matter yield with desirable quality traits for a forage crop. None was ideal and none had a superior combination of traits to the hybrids with Brussels sprouts. The hybrids between marrow-stem kale and January King cabbage were the shortest and a possible alternative to dwarf thousand-head kale. The results can be used to justify new forage brassica breeding programmes. Full article
20 pages, 4629 KiB  
Article
Comprehensive Analysis of Differentially Expressed Genes and Epigenetic Modification-Related Expression Variation Induced by Saline Stress at Seedling Stage in Fiber and Oil Flax, Linum usitatissimum L.
by Ningning Wang, Yujie Lin, Fan Qi, Chunxiao Xiaoyang, Zhanwu Peng, Ying Yu, Yingnan Liu, Jun Zhang, Xin Qi, Michael Deyholos and Jian Zhang
Plants 2022, 11(15), 2053; https://doi.org/10.3390/plants11152053 - 5 Aug 2022
Cited by 7 | Viewed by 1786
Abstract
The ability of different germplasm to adapt to a saline–alkali environment is critical to learning about the tolerance mechanism of saline–alkali stress in plants. Flax is an important oil and fiber crop in many countries. However, its molecular tolerance mechanism under saline stress [...] Read more.
The ability of different germplasm to adapt to a saline–alkali environment is critical to learning about the tolerance mechanism of saline–alkali stress in plants. Flax is an important oil and fiber crop in many countries. However, its molecular tolerance mechanism under saline stress is still not clear. In this study, we studied morphological, physiological characteristics, and gene expression variation in the root and leaf in oil and fiber flax types under saline stress, respectively. Abundant differentially expressed genes (DEGs) induced by saline stress, tissue/organ specificity, and different genotypes involved in plant hormones synthesis and metabolism and transcription factors and epigenetic modifications were detected. The present report provides useful information about the mechanism of flax response to saline stress and could lead to the future elucidation of the specific functions of these genes and help to breed suitable flax varieties for saline/alkaline soil conditions. Full article
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13 pages, 718 KiB  
Article
Morpho-Agronomic and Biochemical Characterization of Accessions of Tiger Nut (Cyperus esculentus) Grown in the North Temperate Zone of China
by Xiangdong Yang, Lu Niu, Yuanyu Zhang, Wei Ren, Chunming Yang, Jing Yang, Guojie Xing, Xiaofang Zhong, Jun Zhang, Jan Slaski and Jian Zhang
Plants 2022, 11(7), 923; https://doi.org/10.3390/plants11070923 - 29 Mar 2022
Cited by 15 | Viewed by 2724
Abstract
Tiger nut (Cyperus esculentus L.) has recently attracted increasing interest from scientific and technological communities because of its potential for serving as additional source of food, oil, and feed. The present study reports morphology and biochemical characterization of 42 tiger nut accessions [...] Read more.
Tiger nut (Cyperus esculentus L.) has recently attracted increasing interest from scientific and technological communities because of its potential for serving as additional source of food, oil, and feed. The present study reports morphology and biochemical characterization of 42 tiger nut accessions collected from China and other counties performed in the 2020 and 2021 growing seasons at Nongan, Jilin Province. Assessment of variability of 14 agronomic traits including plant height, maturation, leaf width, tilling number, color, size, and shape: 100-tuber weight showed a wide range of phenotypic variation. The color, size, and shape and maturation of the tubers, as well as the leaf width, were the most distinct characteristics describing variation among the accessions. Compositional analyses of major nutritional components of the tubers reveals that this crop could be a source of high-value proteins, fatty acids, and carbohydrates. Specifically, tiger nut tubers contained high levels of starch, oil, and sugars, and significant amounts of fiber, Ca, P, and Na. Furthermore, the tubers appeared to be a good source of proteins as they contain 16 amino acids, including the essential ones. Amino acid profiles were dominated by aspartic acid followed by glutamic acid, leucine, alanine, and arginine. Overall, these results demonstrated that tiger nut is well adapted to the temperature and light conditions in the north temperate zone of China, even with a shorter growth season. The tiger nut accessions collected here exhibited wide variations for agronomical and biochemical traits, suggesting potential for potential for breeding improvement by maximizing the fresh tuber and grass yield based on the optimal selection of genetic characteristics in climate and soil conditions of northern China. Full article
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18 pages, 4002 KiB  
Article
Assessing the Response of Diverse Sesame Genotypes to Waterlogging Durations at Different Plant Growth Stages
by Mohammad Habibullah, Shahnaz Sarkar, Mohammad Mahbub Islam, Kamal Uddin Ahmed, Md. Zillur Rahman, Mohamed F. Awad, Abdelaleim I. ElSayed, Elsayed Mansour and Md. Sazzad Hossain
Plants 2021, 10(11), 2294; https://doi.org/10.3390/plants10112294 - 25 Oct 2021
Cited by 22 | Viewed by 3002
Abstract
Sesame is sensitive to waterlogging, and its growth is devastatingly impacted under excess moisture conditions. Thus, waterlogging tolerance is crucial to alleviate yield constraints, particularly under expected climate change. In this study, 119 diverse sesame genotypes were screened for their tolerance to 12, [...] Read more.
Sesame is sensitive to waterlogging, and its growth is devastatingly impacted under excess moisture conditions. Thus, waterlogging tolerance is crucial to alleviate yield constraints, particularly under expected climate change. In this study, 119 diverse sesame genotypes were screened for their tolerance to 12, 24, 48, and 72 h of waterlogging relative to non-waterlogged conditions. All plants died under 72 h of waterlogging, while 13.45%, 31.93%, and 45.38% of genotypes survived at 48, 24, and 12 h, respectively. Based on the seedling parameters and waterlogging tolerance coefficients, genotypes BD-7008 and BD-6985 exhibited the highest tolerance to waterlogging, while BD-6996 and JP-01811 were the most sensitive ones. The responses of these four genotypes to waterlogged conditions were assessed at different plant growth stages—30, 40, and 50 days after sowing (DAS)—versus normal conditions. Waterlogging, particularly when it occurred within 30 DAS, destructively affected the physiological and morphological characteristics, which was reflected in the growth and yield attributes. Genotype BD-7008, followed by BD-6985, exhibited the highest chlorophyll and proline contents as well as enzymatic antioxidant activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). These biochemical and physiological adjustments ameliorated the adverse effects of waterlogging, resulting in higher yields for both genotypes. Conversely, JP-01811 presented the lowest chlorophyll and proline contents as well as enzymatic antioxidant activities, resulting in the poorest growth and seed yield. Full article
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Review

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14 pages, 1320 KiB  
Review
Cell Membrane Features as Potential Breeding Targets to Improve Cold Germination Ability of Seeds
by Lakhvir Kaur Dhaliwal and Rosalyn B. Angeles-Shim
Plants 2022, 11(23), 3400; https://doi.org/10.3390/plants11233400 - 6 Dec 2022
Cited by 10 | Viewed by 3147
Abstract
Cold stress breeding that focuses on the improvement of chilling tolerance at the germination stage is constrained by the complexities of the trait which involves integrated cellular, biochemical, hormonal and molecular responses. Biological membrane serves as the first line of plant defense under [...] Read more.
Cold stress breeding that focuses on the improvement of chilling tolerance at the germination stage is constrained by the complexities of the trait which involves integrated cellular, biochemical, hormonal and molecular responses. Biological membrane serves as the first line of plant defense under stress. Membranes receive cold stress signals and transduce them into intracellular responses. Low temperature stress, in particular, primarily and effectively affects the structure, composition and properties of cell membranes, which ultimately disturbs cellular homeostasis. Under cold stress, maintenance of membrane integrity through the alteration of membrane lipid composition is of prime importance to cope with the stress. This review describes the critical role of cell membranes in cold stress responses as well as the physiological and biochemical manifestations of cold stress in plants. The potential of cell membrane properties as breeding targets in developing strategies to improve cold germination ability is discussed using cotton (Gossypium hirsutum L.) as a model. Full article
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