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Exploring Genes for Crop Breeding and Improvement

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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 (30 October 2023) | Viewed by 27904

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Special Issue Editors

Dr. Prakit Somta

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Guest Editor

Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Bangkok 73140, Thailand
Interests: plant breeding; plant genetic resources; legumes; molecular breeding; QTL

Dr. Tomoki Hoshino

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Guest Editor

Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
Interests: crop breeding; gene; eating quality; mutagenesis; rice; seed quality; soybean; QTL

Dr. Eri Ogiso-Tanaka

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Guest Editor

Center for Molecular Biodiversity Research, National Museum of Nature & Science, Tsukuba 305-0005, Japan
Interests: molecular genetics; molecular breeding; QTL; genetic diversity; plant disease resistance; stress tolerance

Special Issue Information

Dear Colleagues,

Crops have been domesticated over hundreds and thousands of years due to human discovery and selection. Today, the world’s population is growing rapidly, and environmental degradation and outbreaks of pests and diseases are significantly affecting crops. By 2050, the world’s population will reach 9.1 billion, and food production will need to increase to 1.7 times its current level to meet the growing demand for food. Currently, there is an urgent need for crop breeding and improvement to increase food productivity and quality. Recent technological advances have led to rapid progress in the exploration and discovery of genes for crop breeding and improvement, regardless of the genome size in crop. New technologies are also advancing the search for useful genes from underutilized plant genetic resources.

This Special Issue on “Exploring Genes for Crop Breeding and Improvement” will include papers on both basic and applied research highlighting all aspects of crop breeding, from genome sequencing to DNA marker development, the identification of QTLs or genes, genetic engineering, and the development of new technologies related to gene discovery for the breeding and improvement of various crops, including horticultural crops.

Dr. Prakit Somta
Dr. Tomoki Hoshino
Dr. Eri Ogiso-Tanaka
Guest Editors

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Keywords

gene
QTL
genome
plant breeding
plant genetics
genetic engineering
MAS
mutation
diploid
autopolyploid
allopolyploid

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Published Papers (10 papers)

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Research

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19 pages, 4685 KiB

Open AccessArticle

Identification of Genes Responsible for the Synthesis of Glycitein Isoflavones in Soybean Seeds

by Masaki Horitani, Risa Yamada, Kanami Taroura, Akari Maeda, Toyoaki Anai and Satoshi Watanabe

Plants 2024, 13(2), 156; https://doi.org/10.3390/plants13020156 - 5 Jan 2024

Cited by 3 | Viewed by 2108

Abstract

Soybean (Glycine max (L.) Merrill) isoflavones are among the most important secondary metabolites, with functional benefits for human health. Soybeans accumulate three aglycone forms of isoflavones: genistein, daidzein, and glycitein. Soybean landrace Kumachi-1 does not accumulate malonylglycitin at all. Gene structure analysis indicated that Glyma.11G108300 (F6H4) of Kumachi-1 has a 3.8-kbp insertion, resulting in a truncated flavonoid 6-hydroxylase (F6H) sequence compared to the wild-type sequence in Fukuyutaka. Mapping experiments using a mutant line (MUT1246) with a phenotype similar to that of Kumachi-1, with a single-nucleotide polymorphism (SNP) in F6H4, revealed co-segregation of this mutation and the absence of glycitein isoflavones. We also identified a mutant line (K01) that exhibited a change in the HPLC retention time of glycitein isoflavones, accumulating glycoside and malonylglycoside forms of 6-hydroxydaidzein. K01 contains an SNP that produces a premature stop codon in Glyma.01G004200 (IOMT3), a novel soybean isoflavone O-methyltransferase (IOMT) gene. We further analyzed transgenic hairy roots of soybeans expressing Glyma.11G108300 (F6H4) and Glyma.01G004200 (IOMT3). Those overexpressing F6H4 accumulated malonylglycoside forms of 6-hydroxydaidzein (M_6HD), and co-expression of F6H4 and IOMT3 increased the level of malonylglycitin but not of M_6HD. These results indicate that F6H4 and IOMT3 are responsible for glycitein biosynthesis in soybean seed hypocotyl. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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14 pages, 3566 KiB

Open AccessArticle

Effects of Climate Conditions before Harvest Date on Edamame Metabolome

by Akira Oikawa, Katsutaka Takeuchi, Kei Morita, Yamato Horibe, Ryosuke Sasaki and Hideki Murayama

Plants 2024, 13(1), 87; https://doi.org/10.3390/plants13010087 - 27 Dec 2023

Cited by 1 | Viewed by 1638

Abstract

Edamame is a green soybean that is rich in nutrients. Boiled edamame has been traditionally used for food in the East Asia region. It was known among farmers that conditions, such as temperature and climate on the day of harvest, affect the quality of edamame. Large-scale farmers harvest edamame on multiple days in the same year; however, the quality of edamame varies from day to day due to variations in climate conditions. In this study, we harvested edamame over several days between 2013 and 2018, obtained the climate conditions on the harvest date, and performed metabolome analysis using capillary electrophoresis mass spectrometry. To clarify the correlation between climate conditions before the harvest date and edamame components, comparative analyses of the obtained meteorological and metabolomic data were conducted. We found positive and negative correlations between the sunshine duration and average temperature, and the amounts of some edamame components. Furthermore, correlations were observed between the annual fluctuations in climate conditions and edamame components. Our findings suggest that the climate conditions before the date of harvesting are closely related to edamame quality. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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21 pages, 3801 KiB

Open AccessArticle

Genome-Wide Association Analysis of Freezing Tolerance and Winter Hardiness in Winter Wheat of Nordic Origin

by Gabija Vaitkevičiūtė, Aakash Chawade, Morten Lillemo, Žilvinas Liatukas, Andrius Aleliūnas and Rita Armonienė

Plants 2023, 12(23), 4014; https://doi.org/10.3390/plants12234014 - 29 Nov 2023

Cited by 4 | Viewed by 2110

Abstract

Climate change and global food security efforts are driving the need for adaptable crops in higher latitude temperate regions. To achieve this, traits linked with winter hardiness must be introduced in winter-type crops. Here, we evaluated the freezing tolerance (FT) of a panel of 160 winter wheat genotypes of Nordic origin under controlled conditions and compared the data with the winter hardiness of 74 of these genotypes from a total of five field trials at two locations in Norway. Germplasm with high FT was identified, and significant differences in FT were detected based on country of origin, release years, and culton type. FT measurements under controlled conditions significantly correlated with overwintering survival scores in the field (r ≤ 0.61) and were shown to be a reliable complementary high-throughput method for FT evaluation. Genome-wide association studies (GWAS) revealed five single nucleotide polymorphism (SNP) markers associated with FT under controlled conditions mapped to chromosomes 2A, 2B, 5A, 5B, and 7A. Field trials yielded 11 significant SNP markers located within or near genes, mapped to chromosomes 2B, 3B, 4A, 5B, 6B, and 7D. Candidate genes identified in this study can be introduced into the breeding programs of winter wheat in the Nordic region. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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14 pages, 2774 KiB

Open AccessArticle

A Gene Encoding Xylanase Inhibitor Is a Candidate Gene for Bruchid (Callosobruchus spp.) Resistance in Zombi Pea (Vigna vexillata (L.) A. Rich)

by Kitiya Amkul, Kularb Laosatit, Yun Lin, Xingxing Yuan, Xin Chen and Prakit Somta

Plants 2023, 12(20), 3602; https://doi.org/10.3390/plants12203602 - 18 Oct 2023

Cited by 2 | Viewed by 1446

Abstract

Two bruchid species, Callosobruchus maculatus and Callosobruchus chinensis, are the most significant stored insect pests of tropical legume crops. Previously, we identified a major QTL, qBr6.1, controlling seed resistance to these bruchids in the cultivated zombi pea (Vigna vexillata) accession ‘TVNu 240’. In this study, we have narrowed down the qBr6.1 region and identified a candidate gene conferring this resistance. Fine mapping using F₂ and F_2:3 populations derived from a cross between TVNu 240 and TVNu 1623 (susceptible) revealed the existence of two tightly linked QTLs, designated qBr6.1-A and qBr6.1-B, within the qBr6.1. The QTLs qBr6.1-A and qBr6.1-B explained 37.46% and 10.63% of bruchid resistance variation, respectively. qBr6.1-A was mapped to a 28.24 kb region containing four genes, from which the gene VvTaXI encoding a xylanase inhibitor was selected as a candidate gene responsible for the resistance associated with the qBr6.1-A. Sequencing and sequence alignment of VvTaXI from TVNu 240 and TVNu 1623 revealed a 1-base-pair insertion/deletion and five single-nucleotide polymorphisms (SNPs) in the 5′ UTR and 11 SNPs in the exon. Alignment of the VvTAXI protein sequences showed five amino acid changes between the TVNu 240 and TVNu 1623 sequences. Altogether, these results demonstrated that the VvTaXI encoding xylanase inhibitor is the candidate gene conferring bruchid resistance in the zombi pea accession TVNu 240. The gene VvTaXI will be useful for the molecular breeding of bruchid resistance in the zombi pea. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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14 pages, 5293 KiB

Open AccessArticle

Development of a High-Quality/Yield Long-Read Sequencing-Adaptable DNA Extraction Method for Crop Seeds

by Naohiro Shioya, Eri Ogiso-Tanaka, Masanori Watanabe, Toyoaki Anai and Tomoki Hoshino

Plants 2023, 12(16), 2971; https://doi.org/10.3390/plants12162971 - 17 Aug 2023

Cited by 2 | Viewed by 2768

Abstract

Genome sequencing is important for discovering critical genes in crops and improving crop breeding efficiency. Generally, fresh, young leaves are used for DNA extraction from plants. However, seeds, the storage form, are more efficient because they do not require cultivation and can be ground at room temperature. Yet, only a few DNA extraction kits or methods suitable for seeds have been developed to date. In this study, we introduced an improved (IMP) Boom method that is relatively low-cost, simple to operate, and yields high-quality DNA that can withstand long-read sequencing. The method successfully extracted approximately 8 µg of DNA per gram of seed weight from soybean seeds at an average concentration of 48.3 ng/µL, approximately 40-fold higher than that extracted from seeds using a common extraction method kit. The A_260/280 and A_260/230 values of the DNA were 1.90 and 2.43, respectively, which exceeded the respective quality thresholds of 1.8 and 2.0. The DNA also had a DNA integrity number value (indicating the degree of DNA degradation) of 8.1, higher than that obtained using the kit and cetyltrimethylammonium bromide methods. Furthermore, the DNA showed a read length N₅₀ of 20.96 kbp and a maximum read length of 127.8 kbp upon long-read sequencing using the Oxford Nanopore sequencer, with both values being higher than those obtained using the other methods. DNA extracted from seeds using the IMP Boom method showed an increase in the percentage of the nuclear genome with a decrease in the relative ratio of chloroplast DNA. These results suggested that the proposed IMP Boom method can extract high-quality and high-concentration DNA that can be used for long-read sequencing, which cannot be achieved from plant seeds using other conventional DNA extraction methods. The IMP Boom method could also be adapted to crop seeds other than soybeans, such as pea, okra, maize, and sunflower. This improved method is expected to improve the efficiency of various crop-breeding operations, including seed variety determination, testing of genetically modified seeds, and marker-assisted selection. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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15 pages, 3191 KiB

Open AccessArticle

Genetic Mapping of Seven Kinds of Locus for Resistance to Asian Soybean Rust

by Naoki Yamanaka, Luciano N. Aoyagi, Md. Motaher Hossain, Martina B. F. Aoyagi and Yukie Muraki

Plants 2023, 12(12), 2263; https://doi.org/10.3390/plants12122263 - 9 Jun 2023

Cited by 3 | Viewed by 3130

Abstract

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is one of the most serious soybean (Glycine max) diseases in tropical and subtropical regions. To facilitate the development of resistant varieties using gene pyramiding, DNA markers closely linked to seven resistance genes, namely, Rpp1, Rpp1-b, Rpp2, Rpp3, Rpp4, Rpp5, and Rpp6, were identified. Linkage analysis of resistance-related traits and marker genotypes using 13 segregating populations of ASR resistance, including eight previously published by our group and five newly developed populations, identified the resistance loci with markers at intervals of less than 2.0 cM for all seven resistance genes. Inoculation was conducted of the same population with two P. pachyrhizi isolates of different virulence, and two resistant varieties, ‘Kinoshita’ and ‘Shiranui,’ previously thought to only harbor Rpp5, was found to also harbor Rpp3. Markers closely linked to the resistance loci identified in this study will be used for ASR-resistance breeding and the identification of the genes responsible for resistance. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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17 pages, 1983 KiB

Open AccessArticle

Unique Salt-Tolerance-Related QTLs, Evolved in Vigna riukiuensis (Na⁺ Includer) and V. nakashimae (Na⁺ Excluder), Shed Light on the Development of Super-Salt-Tolerant Azuki Bean (V. angularis) Cultivars

by Eri Ogiso-Tanaka, Sompong Chankaew, Yutaro Yoshida, Takehisa Isemura, Rusama Marubodee, Alisa Kongjaimun, Akiko Baba-Kasai, Kazutoshi Okuno, Hiroshi Ehara and Norihiko Tomooka

Plants 2023, 12(8), 1680; https://doi.org/10.3390/plants12081680 - 17 Apr 2023

Cited by 5 | Viewed by 2258

Abstract

Wild relatives of crops have the potential to improve food crops, especially in terms of improving abiotic stress tolerance. Two closely related wild species of the traditional East Asian legume crops, Azuki bean (Vigna angularis), V. riukiuensis “Tojinbaka” and V. nakashimae “Ukushima” were shown to have much higher levels of salt tolerance than azuki beans. To identify the genomic regions responsible for salt tolerance in “Tojinbaka” and “Ukushima”, three interspecific hybrids were developed: (A) azuki bean cultivar “Kyoto Dainagon” × “Tojinbaka”, (B) “Kyoto Dainagon” × “Ukushima” and (C) “Ukushima” × “Tojinbaka”. Linkage maps were developed using SSR or restriction-site-associated DNA markers. There were three QTLs for “percentage of wilt leaves” in populations A, B and C, while populations A and B had three QTLs and population C had two QTLs for “days to wilt”. In population C, four QTLs were detected for Na⁺ concentration in the primary leaf. Among the F₂ individuals in population C, 24% showed higher salt tolerance than both wild parents, suggesting that the salt tolerance of azuki beans can be further improved by combining the QTL alleles of the two wild relatives. The marker information would facilitate the transfer of salt tolerance alleles from “Tojinbaka” and “Ukushima” to azuki beans. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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Review

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16 pages, 2752 KiB

Open AccessReview

Crop Evolution of Foxtail Millet

by Kenji Fukunaga and Makoto Kawase

Plants 2024, 13(2), 218; https://doi.org/10.3390/plants13020218 - 12 Jan 2024

Cited by 4 | Viewed by 3268

Abstract

Studies on the domestication, genetic differentiation, and crop evolution of foxtail millet are reviewed in this paper. Several genetic studies were carried out to elucidate the genetic relationships among foxtail millet accessions originating mainly from Eurasia based on intraspecific hybrid pollen semi-sterility, isozymes, DNA markers, and single-nucleotide polymorphisms. Most studies suggest that China is the center of diversity of foxtail millet, and landraces were categorized into geographical groups. These results indicate that this millet was domesticated in China and spread over Eurasia, but independent origin in other regions cannot be ruled out. Furthermore, the evolution of genes was reviewed (i.e., the Waxy gene conferring amylose content in the endosperm, the Si7PPO gene controlling polyphenol oxidase, the HD1 and SiPRR37 genes controlling heading time, the Sh1 and SvLes1 genes involved in grain shattering, and the C gene controlling leaf sheath pigmentation), and the variation and distribution of these genes suggested complex patterns of evolution under human and/or natural selection. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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16 pages, 3046 KiB

Open AccessReview

Overcoming Difficulties in Molecular Biological Analysis through a Combination of Genetic Engineering, Genome Editing, and Genome Analysis in Hexaploid Chrysanthemum morifolium

by Katsutomo Sasaki and Tsuyoshi Tanaka

Plants 2023, 12(13), 2566; https://doi.org/10.3390/plants12132566 - 6 Jul 2023

Cited by 3 | Viewed by 2475

Abstract

Chrysanthemum is one of the most commercially important ornamental plants globally, of which many new varieties are produced annually. Among these new varieties, many are the result of crossbreeding, while some are the result of mutation breeding. Recent advances in gene and genome sequencing technology have raised expectations about the use of biotechnology and genome breeding to efficiently breed new varieties. However, some features of chrysanthemum complicate molecular biological analysis. For example, chrysanthemum is a hexaploid hyperploid plant with a large genome, while its genome is heterogeneous because of the difficulty of obtaining pure lines due to self-incompatibility. Despite these difficulties, an increased number of reports on transcriptome analysis in chrysanthemum have been published as a result of recent technological advances in gene sequencing, which should deepen our understanding of the properties of these plants. In this review, we discuss recent studies using gene engineering, genome editing, and genome analysis, including transcriptome analysis, to analyze chrysanthemum, as well as the current status of and future prospects for chrysanthemum. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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12 pages, 698 KiB

Open AccessReview

Somatic Mutations in Fruit Trees: Causes, Detection Methods, and Molecular Mechanisms

by Seunghyun Ban and Je Hyeong Jung

Plants 2023, 12(6), 1316; https://doi.org/10.3390/plants12061316 - 14 Mar 2023

Cited by 11 | Viewed by 5198

Abstract

Somatic mutations are genetic changes that occur in non-reproductive cells. In fruit trees, such as apple, grape, orange, and peach, somatic mutations are typically observed as “bud sports” that remain stable during vegetative propagation. Bud sports exhibit various horticulturally important traits that differ from those of their parent plants. Somatic mutations are caused by internal factors, such as DNA replication error, DNA repair error, transposable elements, and deletion, and external factors, such as strong ultraviolet radiation, high temperature, and water availability. There are several methods for detecting somatic mutations, including cytogenetic analysis, and molecular techniques, such as PCR-based methods, DNA sequencing, and epigenomic profiling. Each method has its advantages and limitations, and the choice of method depends on the research question and the available resources. The purpose of this review is to provide a comprehensive understanding of the factors that cause somatic mutations, techniques used to identify them, and underlying molecular mechanisms. Furthermore, we present several case studies that demonstrate how somatic mutation research can be leveraged to discover novel genetic variations. Overall, considering the diverse academic and practical value of somatic mutations in fruit crops, especially those that require lengthy breeding efforts, related research is expected to become more active. Full article

(This article belongs to the Special Issue Exploring Genes for Crop Breeding and Improvement)

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