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Crop Genomics and Breeding
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Crop Genomics and Breeding

A topical collection in Plants (ISSN 2223-7747). This collection belongs to the section "Plant Molecular Biology".

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Editors

Prof. Dr. Changsoo Kim

E-Mail Website
Collection Editor
Department of Crop Science, Chungnam National University, Daejeon 34134, Republic of Korea
Interests: structural genomics; comparative genomics; evolution; breeding; poaceae
Prof. Dr. Kyung Do Kim

E-Mail Website
Collection Editor
Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058, Korea
Interests: soybean; genomics; epigenomics
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

With the advent of next-generation sequencing technology, genomics has been receiving intensive attention for the last two decades. In fact, since the Arabidopsis genome was completed, draft sequences of pseudomolecules have been published for more than 100 plant genomes, including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, the recurring complication in crop genotyping that differs from other taxa is a high level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. Nonetheless, advanced genomics technologies have facilitated new opportunities for breeders with a cost-effective, genome-wide scanning, and multiplexed sequencing platform, being able to contribute to many crop breeding programs.

One of the global key phrases in the 21st century is feeding the world. However, foreseeable climate changes can dramatically reduce agricultural productivity, mainly due to abiotic and biotic stresses. To meet the global food demand of an increasing population, food production has to be increased by 60% by 2050. With limited agricultural land, innovative crop cultivation together with the breeding of improved cultivars may be required for resolving the largest part of food security issues.

Plant breeding generally requires the analysis of the genetic background of a target species. In conventional breeding, farmers or breeders traditionally utilized phenotypic markers for selecting desirable plants; however, the use of molecular markers has dramatically changed the landscape of plant breeding. Molecular markers have a number of advantages in plant science in that they are (1) not subject to environmental influence, (2) theoretically available in vast numbers, and (3) usually more objective than phenotypic markers. Consequently, molecular markers can be used for marker-assisted selection (MAS) to greatly increase the efficiency and precision of plant breeding compared to conventional methods. In particular, a plethora of genome data has facilitated the application of sequence-based markers such as simple sequence repeats (SSRs) and SNPs. The frequent use of genomic resources for plant breeding has led to the creation of a new term, genomics-assisted breeding (GAB), integrating all genomics tools and resources. In addition, we are facing a new breeding paradigm, genome selection (GS), by virtue of overflowing genomic and phenotypic data.

With this background, we welcome eminent researchers working on crop genomics across the world to contribute their high-quality original research manuscripts, critical reviews, and opinion articles covering all modern crop genomics and breeding:

  • Plant research focusing on food crops including structural, functional, comparative, and evolutionary genomics;
  • Application of new genotyping tools;
  • Application of genomic tools in plant breeding;
  • Genome-wide association study (GWAS) and genetic dissection of complex traits;
  • Genome selection and predictive breeding;
  • Integration of multi-omics data for prediction of plant phenotypes;
  • New breeding techniques for introduction of novel alleles;
  • Plant epigenomics research and its potential application in crop improvement.

Prof. Dr. Changsoo Kim
Prof. Dr. Kyung Do Kim
Collection Editors

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Keywords

  • plant genome
  • genomics-assisted breeding
  • genome prediction
  • sequencing
  • bioinformatics

Published Papers (14 papers)

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2023

Jump to: 2022, 2021, 2020

16 pages, 1840 KiB  
Article
An Interdisciplinary Assessment of Biochemical and Antioxidant Attributes of Six Greek Vicia sativa L. Varieties
by Eleni D. Myrtsi, Dimitrios N. Vlachostergios, Christos Petsoulas, Epameinondas Evergetis, Sofia D. Koulocheri and Serkos A. Haroutounian
Plants 2023, 12(15), 2807; https://doi.org/10.3390/plants12152807 - 28 Jul 2023
Viewed by 698
Abstract
Common vetch (Vicia sativa L.) is one of the most cultivated feed crops with extensive agricultural diversity and numerous cultivars. This study concerns the first-time investigation of the dry plant biomass and grains of six vetch cultivars to define the detailed fingerprint [...] Read more.
Common vetch (Vicia sativa L.) is one of the most cultivated feed crops with extensive agricultural diversity and numerous cultivars. This study concerns the first-time investigation of the dry plant biomass and grains of six vetch cultivars to define the detailed fingerprint of their phenolic and fatty acid content, along with their respective antioxidant potencies. The results revealed a substantial variation in the feed quality traits among the tested Vicia sativa varieties, highlighting the crucial role and influence the genotype plays in the achievement of high-quality livestock nutrition. Among the six varieties tested, Istros and M-6900 displayed a particularly intriguing phytochemical profile characterized by elevated phenolic content, significant antioxidant potency and remarkably high fatty acid indices. These findings are indicative of the great potential of these varieties to function as suitable candidates for incorporation into farm animal diets either in the form of dry biomass (hay) or as a grain feed additive. Full article
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2022

Jump to: 2023, 2021, 2020

16 pages, 4231 KiB  
Article
Pyramiding of Four Broad Spectrum Bacterial Blight Resistance Genes in Cross Breeds of Basmati Rice
by Irfan Ullah, Hamid Ali, Tariq Mahmood, Mudassar Nawaz Khan, Muhammad Haris, Hussain Shah, Adil Mihoub, Aftab Jamal, Muhammad Farhan Saeed, Roberto Mancinelli and Emanuele Radicetti
Plants 2023, 12(1), 46; https://doi.org/10.3390/plants12010046 - 22 Dec 2022
Cited by 4 | Viewed by 2120
Abstract
Pyramiding of major resistance (R) genes through marker-assisted selection (MAS) is a useful way to attain durable and broad-spectrum resistance against Xanthomonas oryzae pv. oryzae pathogen, the causal agent of bacterial blight (BB) disease in rice (Oryza sativa L.). The [...] Read more.
Pyramiding of major resistance (R) genes through marker-assisted selection (MAS) is a useful way to attain durable and broad-spectrum resistance against Xanthomonas oryzae pv. oryzae pathogen, the causal agent of bacterial blight (BB) disease in rice (Oryza sativa L.). The present study was designed to pyramid four broad spectrum BB-R genes (Xa4, xa5, xa13 and Xa21) in the background of Basmati-385, an indica rice cultivar with much sought-after qualitative and quantitative grain traits. The cultivar, however, is susceptible to BB and was therefore, crossed with IRBB59 which possesses R genes xa5, xa13 and Xa21, to attain broad and durable resistance. A total of 19 F1 plants were obtained, some of which were backcrossed with Basmati-385 and large number of BC1F1 plants were obtained. In BC1F2 generation, 31 phenotypically superior genotypes having morphological features of Basmati-385, were selected and advanced up to BC1F6 population. Sequence-tagged site (STS)-based MAS was carried out and phenotypic selection was made in each successive generation. In BC1F6 population, potentially homozygous recombinant inbred lines (RILs) from each line were selected and evaluated on the bases of STS evaluation and resistance to local Xanthomonas oryzae pv. oryzae (Xoo) isolates. Line 23 was found pyramided with all four BB-R genes i.e., Xa4, xa5, xa13 and Xa21. Five genotypes including line 8, line 16, line 21, line 27 and line 28 were identified as pyramided with three R genes, Xa4, xa5 and xa13. Pathological study showed that rice lines pyramided with quadruplet or triplet R genes showed the highest level of resistance compared to doublet or singlet R genes. Thus, line 23 with quadruplet, and lines 8, 16, 21, 27, and 28 with triplet R genes, are recommended for replicated yield and resistance trials before release as new rice varieties. Further, traditional breeding coupled with MAS, is a solid way to attain highly effective BB-resistant rice lines with no yield cost. Full article
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23 pages, 2206 KiB  
Article
Expression Profile of Sorghum Genes and Cis-Regulatory Elements under Salt-Stress Conditions
by Solji Lee, Donghyun Jeon, Sehyun Choi, Yuna Kang, Sumin Seo, Soonjae Kwon, Jaeil Lyu, Joonwoo Ahn, Jisu Seo and Changsoo Kim
Plants 2022, 11(7), 869; https://doi.org/10.3390/plants11070869 - 24 Mar 2022
Cited by 2 | Viewed by 2154
Abstract
Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum (Sorghum bicolor (L.) Moench) is one [...] Read more.
Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum (Sorghum bicolor (L.) Moench) is one of the world’s four major grains and is known as a plant with excellent adaptability to salt stress. Among the various genotypes of sorghum, a Korean cultivar Nampungchal is also highly tolerant to salt. However, little is known about how Nampungchal responds to salt stress. In this study, we measured various physiological parameters, including Na+ and K+ contents, in leaves grown under saline conditions and investigated the expression patterns of differentially expressed genes (DEGs) using QuantSeq analysis. These DEG analyses revealed that genes up-regulated in a 150 mM NaCl treatment have various functions related to abiotic stresses, such as ERF and DREB. In addition, transcription factors such as ABA, WRKY, MYB, and bZip bind to the CREs region of sorghum and are involved in the regulation of various abiotic stress-responsive transcriptions, including salt stress. These findings may deepen our understanding of the mechanisms of salt tolerance in sorghum and other crops. Full article
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2021

Jump to: 2023, 2022, 2020

12 pages, 1475 KiB  
Article
Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars
by Youngjun Mo, Chang-Min Lee, Hyang-Mi Park, Su-Kyung Ha, Mi-Jung Kim, Jieun Kwak, Hyun-Sook Lee, Jeong-Heui Lee and Ji-Ung Jeung
Plants 2021, 10(11), 2408; https://doi.org/10.3390/plants10112408 - 08 Nov 2021
Cited by 3 | Viewed by 2173
Abstract
Optimizing flowering time in crop plants is critical for maximizing yield and quality under target environments. While there is a wide range of heading date variation in Korean rice cultivars, the underlying gene mechanisms are unclear. Here, we sequenced the protein coding regions [...] Read more.
Optimizing flowering time in crop plants is critical for maximizing yield and quality under target environments. While there is a wide range of heading date variation in Korean rice cultivars, the underlying gene mechanisms are unclear. Here, we sequenced the protein coding regions of Hd1, the major rice heading date gene, from 293 Korean rice cultivars and investigated the associations between Hd1 allele types and major agronomic traits under four different environments. There were four functional Hd1 and five nonfunctional hd1 alleles distributed among the 293 Korean rice cultivars. The effects of the Hd1 allele types were highly significant for days to heading in all four environments, explaining 51.4–65.8% of the phenotypic variation. On average, cultivars carrying nonfunctional hd1 headed 13.7 days earlier than those carrying functional Hd1. While the Hd1 allele types exhibited highly significant effects on culm length and protein content under all four environments, the differences between cultivars carrying Hd1 and hd1 were minimal. The effects of the Hd1 allele types on amylose content were significant in only one of the four environments. Our results provide useful information for fine-tuning rice heading dates by utilizing different Hd1 alleles in rice breeding programs. Full article
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12 pages, 1678 KiB  
Article
Molecular Characterization of Novel x-Type HMW Glutenin Subunit 1B × 6.5 in Wheat
by Tímea Kuťka Hlozáková, Zdenka Gálová, Svetlana Šliková, Leona Leišová-Svobodová, Jana Beinhauer, Filip Dyčka, Marek Šebela, Erika Zetochová and Edita Gregová
Plants 2021, 10(10), 2108; https://doi.org/10.3390/plants10102108 - 05 Oct 2021
Cited by 1 | Viewed by 1750
Abstract
A novel high molecular weight glutenin subunit encoded by the Glu-1B locus was identified in the French genotype Bagou, which we named 1B × 6.5. This subunit differed in SDS-PAGE from well-known 1B × 6 and 1B × 7 subunits, which are also [...] Read more.
A novel high molecular weight glutenin subunit encoded by the Glu-1B locus was identified in the French genotype Bagou, which we named 1B × 6.5. This subunit differed in SDS-PAGE from well-known 1B × 6 and 1B × 7 subunits, which are also encoded at this locus. Subunit 1B × 6.5 has a theoretical molecular weight of 88,322.83 Da, which is more mobile than 1B × 6 subunit, and isoelectric point (pI) of about 8.7, which is lower than that for 1B × 6 subunit. The specific primers were designed to amplify and sequence 2476 bp of the Glu-1B locus from genotype Bagou. A high level of similarity was found between the sequence encoding 1B × 6.5 and other x-type encoding alleles of this locus. Full article
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20 pages, 1614 KiB  
Article
Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam
by Ngoc Ha Luong, Le-Hung Linh, Kyu-Chan Shim, Cheryl Adeva, Hyun-Sook Lee and Sang-Nag Ahn
Plants 2021, 10(10), 2094; https://doi.org/10.3390/plants10102094 - 03 Oct 2021
Cited by 8 | Viewed by 2409
Abstract
Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many [...] Read more.
Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions. Full article
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13 pages, 2637 KiB  
Article
Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement
by Jae-Sung Lee, Dmytro Chebotarov, Kenneth L. McNally, Valerien Pede, Tri Deri Setiyono, Rency Raquid, Woong-Jo Hyun, Ji-Ung Jeung, Ajay Kohli and Youngjun Mo
Plants 2021, 10(8), 1709; https://doi.org/10.3390/plants10081709 - 19 Aug 2021
Cited by 12 | Viewed by 2839
Abstract
Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible [...] Read more.
Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8–10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways. Full article
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17 pages, 2245 KiB  
Article
Validation of Reference Genes for Studying Different Abiotic Stresses in Oat (Avena sativa L.) by RT-qPCR
by Judit Tajti, Magda Pál and Tibor Janda
Plants 2021, 10(7), 1272; https://doi.org/10.3390/plants10071272 - 22 Jun 2021
Cited by 19 | Viewed by 2288
Abstract
Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value and it is grown mainly in temperate regions. The number of studies dealing with gene expression changes in oat continues to increase, and to obtain reliable RT-qPCR results it [...] Read more.
Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value and it is grown mainly in temperate regions. The number of studies dealing with gene expression changes in oat continues to increase, and to obtain reliable RT-qPCR results it is essential to establish and use reference genes with the least possible influence caused by experimental conditions. However, no detailed study has been conducted on reference genes in different tissues of oat under diverse abiotic stress conditions. In our work, nine candidate reference genes (ACT, TUB, CYP, GAPD, UBC, EF1, TBP, ADPR, PGD) were chosen and analysed by four statistical methods (GeNorm, Normfinder, BestKeeper, RefFinder). Samples were taken from two tissues (leaves and roots) of 13-day-old oat plants exposed to five abiotic stresses (drought, salt, heavy metal, low and high temperatures). ADPR was the top-rated reference gene for all samples, while different genes proved to be the most stable depending on tissue type and treatment combinations. TUB and EF1 were most affected by the treatments in general. Validation of reference genes was carried out by PAL expression analysis, which further confirmed their reliability. These results can contribute to reliable gene expression studies for future research in cultivated oat. Full article
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9 pages, 1133 KiB  
Article
Sinbase 2.0: An Updated Database to Study Multi-Omics in Sesamum indicum
by Liwen Wang, Jingyin Yu, Yanxin Zhang, Jun You, Xiurong Zhang and Linhai Wang
Plants 2021, 10(2), 272; https://doi.org/10.3390/plants10020272 - 30 Jan 2021
Cited by 5 | Viewed by 3244
Abstract
Sesame is one of the oldest oil crops in the world and is widely grown in the tropical and subtropical areas of Asia, Africa and America. Upon the completion of the sesame reference genome version 1.0, we launched Sinbase 1.0 as an integrated [...] Read more.
Sesame is one of the oldest oil crops in the world and is widely grown in the tropical and subtropical areas of Asia, Africa and America. Upon the completion of the sesame reference genome version 1.0, we launched Sinbase 1.0 as an integrated database for genomic and bioinformatics analyses. Recently, an upgraded version (version 2.0) of the genome sequence was released. In addition, large numbers of multi-omics data have been generated on sesame, but a comprehensive database that integrates these resources for the community has been lacking until now. Here, we developed an interactive and comprehensive sesame multi-omics database, Sinbase 2.0, which provides information of the sesame updated genome containing 13 chromosomes, 3 genetic linkage maps, 5 intra- and 6 inter-species comparative genomics, 1 genomic variation analysis, 5 transcriptome data, 1 proteome, 31 functional markers, 175 putative functional genes, and 54 QTLs detected for important agronomic traits. Moreover, Sinbase 2.0 has been enriched with novel user-friendly computational tools. All datasets of Sinbase 2.0 can be downloaded online conveniently. Sinbase 2.0 will be updated regularly with new available sesame multi-omics data and can be accessed freely via Sinbase 2.—Sesame Muti-Omics Database. We expect that Sinbase 2.0, similarly to the previous version, will continue to make a major contribution to advance sesame research towards a better understanding of its biology and genetic improvement, as well as comparative genomics and evolutionary biology. Full article
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2020

Jump to: 2023, 2022, 2021

12 pages, 2734 KiB  
Article
Natural Variation and Domestication Selection of ZmCKX5 with Root Morphological Traits at the Seedling Stage in Maize
by Houmiao Wang, Hui Sun, Haofeng Xia, Tingting Wu, Pengcheng Li, Chenwu Xu and Zefeng Yang
Plants 2021, 10(1), 1; https://doi.org/10.3390/plants10010001 - 22 Dec 2020
Cited by 13 | Viewed by 2194
Abstract
Root system architecture plays a crucial role in water and nutrient acquisition in maize. Cytokinins, which can be irreversibly degraded by the cytokinin oxidase/dehydrogenase (CKX), are important hormones that regulate root development in plants. In this study, ZmCKX5 was resequenced in 285 inbred [...] Read more.
Root system architecture plays a crucial role in water and nutrient acquisition in maize. Cytokinins, which can be irreversibly degraded by the cytokinin oxidase/dehydrogenase (CKX), are important hormones that regulate root development in plants. In this study, ZmCKX5 was resequenced in 285 inbred lines, 68 landraces, and 32 teosintes to identify the significant variants associated with root traits in maize. Sequence polymorphisms and nucleotide diversity revealed that ZmCKX5 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 12 variants of ZmCKX5 that were significantly associated with six root traits, including seed root number (SRN), lateral root length (LRL), total root area (RA), root length in 0 to 0.5 mm diameter class (RL005), total root volume (RV), and total root length (TRL). SNP-1195 explained the most (6.01%) phenotypic variation of SRN, and the frequency of this allele G increased from 6.25% and 1.47% in teosintes and landraces, respectively, to 17.39% in inbred lines. Another significant variant, SNP-1406, with a pleiotropic effect, is strongly associated with five root traits, with the frequency of T allele increased from 25.00% and 23.73% in teosintes and landraces, respectively, to 35.00% in inbred lines. These results indicate that ZmCKX5 may be involved in the development of the maize root system and that the significant variants can be used to develop functional markers to accelerate the improvement in the maize root system. Full article
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15 pages, 3895 KiB  
Article
Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS
by Xiaoping Liu, Hongwei Lu, Panna Liu, Han Miao, Yuling Bai, Xingfang Gu and Shengping Zhang
Plants 2020, 9(12), 1659; https://doi.org/10.3390/plants9121659 - 27 Nov 2020
Cited by 14 | Viewed by 3051
Abstract
Downy mildew (DM) is one of the most serious diseases in cucumber. Multiple quantitative trait loci (QTLs) for DM resistance have been detected in a limited number of cucumber accessions. In this study we applied genome-wide association analysis (GWAS) to detected genetic loci [...] Read more.
Downy mildew (DM) is one of the most serious diseases in cucumber. Multiple quantitative trait loci (QTLs) for DM resistance have been detected in a limited number of cucumber accessions. In this study we applied genome-wide association analysis (GWAS) to detected genetic loci for DM resistance in a core germplasm (CG) of cucumber lines that represent diverse origins and ecotypes. Phenotypic data on responses to DM infection were collected in four field trials across three years, 2014, 2015, and 2016. With the resequencing data of these CG lines, GWAS for DM resistance was performed and detected 18 loci that were distributed on all the seven cucumber chromosomes. Of these 18 loci, only six (dmG1.4, dmG4.1, dmG4.3, dmG5.2, dmG7.1, and dmG7.2) were detected in two experiments, and were considered as loci with a stable effect on DM resistance. Further, 16 out of the 18 loci colocalized with the QTLs that were reported in previous studies and two loci, dmG2.1 and dmG7.1, were novel ones identified only in this study. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, several candidate genes were identified as potential causal genes underlying the stable and novel loci, including Csa1G575030 for dmG1.4, Csa2G060360 for dmG2.1, Csa4G064680 for dmG4.1, Csa5G606470 for dmG5.2, and Csa7G004020 for dmG7.1. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for DM resistance. The potential of using these CG lines for future allele-mining of candidate genes was discussed in the context of breeding cucumber with resistance to DM. Full article
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24 pages, 1417 KiB  
Review
Application of Genomic Big Data in Plant Breeding: Past, Present, and Future
by Kyung Do Kim, Yuna Kang and Changsoo Kim
Plants 2020, 9(11), 1454; https://doi.org/10.3390/plants9111454 - 28 Oct 2020
Cited by 20 | Viewed by 5979
Abstract
Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase [...] Read more.
Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain. Full article
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25 pages, 11162 KiB  
Article
Functional Analysis of StPHT1;7, a Solanum tuberosum L. Phosphate Transporter Gene, in Growth and Drought Tolerance
by Minxuan Cao, Hengzhi Liu, Chao Zhang, Dongdong Wang, Xiaofang Liu and Qin Chen
Plants 2020, 9(10), 1384; https://doi.org/10.3390/plants9101384 - 17 Oct 2020
Cited by 13 | Viewed by 2545
Abstract
PHT1 (phosphate transporter 1) family genes play important roles in regulating plant growth and responding to stress. However, there has been little research on the role of the PHT1 family in potatoes. In this study, using molecular and bioinformatic approaches, 8 PHT1 family [...] Read more.
PHT1 (phosphate transporter 1) family genes play important roles in regulating plant growth and responding to stress. However, there has been little research on the role of the PHT1 family in potatoes. In this study, using molecular and bioinformatic approaches, 8 PHT1 family genes were identified from the potato genome. StPHT1;7 was highly expressed in the whole potato plants. The overexpression and silence vectors of StPHT1;7 were constructed and transformed into the potato cultivar Desiree. Consequently, StPHT1;7 overexpression (with a relative expression 2–7-fold that in the control) and silence lines (with a relative expression of 0.3%–1% that in the control) were obtained. Their growth vigor was ranked in the order overexpression line > wild type > silence line. In the absence of phosphorus, the root length of the overexpression line was approximately 2.6 times that of the wild type, while the root length of the silence line was approximately 0.6 times that of the wild type. Furthermore, their tolerance to drought stress was ranked as wild type > overexpression line > silence line. These results suggest that StPHT1;7 affects growth and stress tolerance in potato plants. Full article
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15 pages, 1140 KiB  
Article
QTL Mapping and Candidate Gene Analysis for Pod Shattering Tolerance in Soybean (Glycine max)
by Jeong-Hyun Seo, Beom-Kyu Kang, Sanjeev K. Dhungana, Jae-Hyeon Oh, Man-Soo Choi, Ji-Hee Park, Sang-Ouk Shin, Hong-Sik Kim, In-Youl Baek, Jung-Sook Sung, Chan-Sik Jung, Ki-Seung Kim and Tae-Hwan Jun
Plants 2020, 9(9), 1163; https://doi.org/10.3390/plants9091163 - 08 Sep 2020
Cited by 8 | Viewed by 3181
Abstract
Pod shattering is an important reproductive process in many wild species. However, pod shattering at the maturing stage can result in severe yield loss. The objectives of this study were to discover quantitative trait loci (QTLs) for pod shattering using two recombinant inbred [...] Read more.
Pod shattering is an important reproductive process in many wild species. However, pod shattering at the maturing stage can result in severe yield loss. The objectives of this study were to discover quantitative trait loci (QTLs) for pod shattering using two recombinant inbred line (RIL) populations derived from an elite cultivar having pod shattering tolerance, namely “Daewonkong”, and to predict novel candidate QTL/genes involved in pod shattering based on their allele patterns. We found several QTLs with more than 10% phenotypic variance explained (PVE) on seven different chromosomes and found a novel candidate QTL on chromosome 16 (qPS-DS16-1) from the allele patterns in the QTL region. Out of the 41 annotated genes in the QTL region, six were found to contain SNP (single-nucleotide polymorphism)/indel variations in the coding sequence of the parents compared to the soybean reference genome. Among the six potential candidate genes, Glyma.16g076600, one of the genes with known function, showed a highly differential expression levels between the tolerant and susceptible parents in the growth stages R3 to R6. Further, Glyma.16g076600 is a homolog of AT4G19230 in Arabidopsis, whose function is related to abscisic acid catabolism. The results provide useful information to understand the genetic mechanism of pod shattering and could be used for improving the efficiency of marker-assisted selection for developing varieties of soybeans tolerant to pod shattering. Full article
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