Breeding SciencePub Date : 2024-03-01Epub Date: 2024-03-20DOI: 10.1270/jsbbs.23058
Navneet Kaur, Natasha Brock, Sarah Raffan, Nigel G Halford
{"title":"Low asparagine wheat: Europe's first field trial of genome edited wheat amid rapidly changing regulations on acrylamide in food and genome editing of crops.","authors":"Navneet Kaur, Natasha Brock, Sarah Raffan, Nigel G Halford","doi":"10.1270/jsbbs.23058","DOIUrl":"10.1270/jsbbs.23058","url":null,"abstract":"<p><p>We review the undertaking of a field trial of low asparagine wheat lines in which the asparagine synthetase gene, <i>TaASN2</i>, has been knocked out using CRISPR/Cas9. The field trial was undertaken in 2021-2022 and represented the first field release of genome edited wheat in Europe. The year of the field trial and the period since have seen rapid changes in the regulations covering both the field release and commercialisation of genome edited crops in the UK. These historic developments are reviewed in detail. Free asparagine is the precursor for acrylamide formation during high-temperature cooking and processing of grains, tubers, storage roots, beans and other crop products. Consequently, work on reducing the free asparagine concentration of wheat and other cereal grains, as well as the tubers, beans and storage roots of other crops, is driven by the need for food businesses to comply with current and potential future regulations on acrylamide content of foods. The topic illustrates how strategic and applied crop research is driven by regulations and also needs a supportive regulatory environment in which to thrive.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 1","pages":"37-46"},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Breeding SciencePub Date : 2024-03-01Epub Date: 2024-04-09DOI: 10.1270/jsbbs.23074
Satoko Nonaka, Hiroshi Ezura
{"title":"Possibility of genome editing for melon breeding.","authors":"Satoko Nonaka, Hiroshi Ezura","doi":"10.1270/jsbbs.23074","DOIUrl":"10.1270/jsbbs.23074","url":null,"abstract":"<p><p>Genome editing technologies are promising for conventional mutagenesis breeding, which takes a long time to remove unnecessary mutations through backcrossing and create new lines because they directly modify the target genes of elite strains. In particular, this technology has advantages for traits caused by the loss of function. Many efforts have been made to utilize this technique to introduce valuable features into crops, including maize, soybeans, and tomatoes. Several genome-edited crops have already been commercialized in the US and Japan. Melons are an important vegetable crop worldwide, produced and used in various areas. Therefore, many breeding efforts have been made to improve its fruit quality, resistance to plant diseases, and stress tolerance. Quantitative trait loci (QTL) analysis was performed, and various genes related to important traits were identified. Recently, several studies have shown that the CRISPR/Cas9 system can be applied to melons, resulting in its possible utilization as a breeding technique. Focusing on two productivity-related traits, disease resistance, and fruit quality, this review introduces the progress in genetics, examples of melon breeding through genome editing, improvements required for breeding applications, and the possibilities of genome editing in melon breeding.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 1","pages":"47-58"},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Estimation of pollen dispersal distance in Job's tears (<i>Coix lacryma-jobi</i> L.) by using red leaf sheath as a morphological marker.","authors":"Katsuhiro Matsui, Takayuki Tamura, Keito Nishizawa, Akiko Ohara-Takada","doi":"10.1270/jsbbs.23016","DOIUrl":"10.1270/jsbbs.23016","url":null,"abstract":"<p><p>Job's tears (<i>Coix lacryma-jobi</i> L.) is grown widely in Asian countries and a crop that can fertilize with own pollen and pistils. The grains are used not only for food but also for medicinal purposes. The grain of many cultivars contains glutinous endosperm; only grains with this glutinous endosperm are suitable for use as medicine in Japan. Many wild types have non-glutinous endosperm and can easily cross with cultivar under natural environmental conditions. Because the non-glutinous endosperm trait is dominant to that of glutinous endosperm, F<sub>1</sub> seeds produced by crosses between a cultivar and a wild type have non-glutinous endosperm. To reduce the rate of unwanted crosses, we investigated the pollen dispersal distance by using a red leaf sheath as a morphological marker. When plants were cultivated in rows 70 cm apart, the crossing rate was about 25%-35%. As the distance increased, the crossing rate decreased at a rate that could be fitted to a power approximation in fields without intervening plants and to an exponential equation in fields with intervening plants. Our data could be used as guidelines for preventing unwanted crossing with wild types when growing cultivars.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"1 1","pages":"408-414"},"PeriodicalIF":2.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66690197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Breeding SciencePub Date : 2023-09-01Epub Date: 2023-09-09DOI: 10.1270/jsbbs.23017
Saw Bo Day Shar, Cuong Dinh Nguyen, Sachiyo Sanada-Morimura, Hideshi Yasui, Shao-Hui Zheng, Daisuke Fujita
{"title":"Development and characterization of near-isogenic lines for brown planthopper resistance genes in the genetic background of <i>japonica</i> rice 'Sagabiyori'.","authors":"Saw Bo Day Shar, Cuong Dinh Nguyen, Sachiyo Sanada-Morimura, Hideshi Yasui, Shao-Hui Zheng, Daisuke Fujita","doi":"10.1270/jsbbs.23017","DOIUrl":"10.1270/jsbbs.23017","url":null,"abstract":"<p><p>The brown planthopper (BPH: <i>Nilaparvata lugens</i> Stål) is one of the most destructive insects in rice production. The use of host plant resistance has potential to reduce damage caused by BPH. The heat tolerance <i>japonica</i> rice 'Sagabiyori', with superior grain quality and high soluble starch in the stem, is highly susceptible to damage by BPH. Here, to enhance its BPH resistance, we developed seven near-isogenic lines (NILs) carrying <i>BPH2</i>, <i>BPH17-ptb</i>, <i>BPH32</i>, <i>BPH3</i>, <i>BPH17</i>, <i>BPH20</i>, and <i>BPH21</i> through marker-assisted selection and evaluated resistance to two BPH populations. Most lines were more resistant to the Hadano-1966 BPH population than Sagabiyori but were less effective against the highly virulent Koshi-2013 population. Nevertheless, in antixenosis tests, Koshi-2013 settled less on all NILs than on Sagabiyori. In addition, adult mortality and the percentage of fresh weight loss of lines carrying <i>BPH17</i> and <i>BPH3</i> indicated that these lines have higher resistance to Koshi-2013 than Sagabiyori. Current study revealed that BPH resistance of Sagabiyori became stronger by transferring <i>BPH3</i> and <i>BPH17</i> genes. Thus, <i>BPH3</i> and <i>BPH17</i> might be valuable for breeding programs to enhance BPH resistance of high grain quality rice varieties with heat tolerance.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"1 1","pages":"382-392"},"PeriodicalIF":2.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66690304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Breeding SciencePub Date : 2023-09-01Epub Date: 2023-09-09DOI: 10.1270/jsbbs.23022
Tatsuro Murata
{"title":"Histological studies on the relationship between the low seed set and abnormal embryo sacs in sweet potato, <i>Ipomoea batatas</i> (L.) Lam.","authors":"Tatsuro Murata","doi":"10.1270/jsbbs.23022","DOIUrl":"10.1270/jsbbs.23022","url":null,"abstract":"<p><p>This study aimed to investigate the relationship between low seed set and abnormal embryo sacs lacking normal female organs, such as one egg cell, two assistant cells, and two polar nuclei, in <i>Ipomoea trifida</i>, which is closely related to sweet potato, and sweet potato cultivars and lines, through histological analysis of their ovaries on flowering day. Ovaries of diploid, tetraploid, and hexaploid lines of <i>I. trifida</i> each had four ovules, except for some hexaploid lines with five or six ovules. Almost all sweet potato cultivars and lines had four ovules per ovary, although some sib-cross lines had two or three ovules. The number of ovules per ovary did not have direct effects on low seed set. The frequency of abnormal embryo sac increased with polyploidy in <i>I. trifida</i>. However, it varied among different sweet potato cultivars and lines. Moreover, the variation in abnormal embryo sacs occurred at an earlier stage of gametogenesis (type A) in the tetraploid and hexaploid plants of <i>I. trifida</i> and sweet potato cultivars and lines. These findings suggest that the high frequency of abnormal embryo sacs is a primary cause of low seed set in sweet potato and that it is closely related to the decline in seed propagation that occurs in the evolution process of sweet potato.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"1 1","pages":"393-400"},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66690473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"V-primer: software for the efficient design of genome-wide InDel and SNP markers from multi-sample variant call format (VCF) genotyping data.","authors":"Satoshi Natsume, Kaori Oikawa, Chihiro Nomura, Kazue Ito, Hiroe Utsushi, Motoki Shimizu, Ryohei Terauchi, Akira Abe","doi":"10.1270/jsbbs.23018","DOIUrl":"10.1270/jsbbs.23018","url":null,"abstract":"<p><p>DNA markers are indispensable tools in genetics and genomics research as well as in crop breeding, particularly for marker-assisted selection. Recent advances in next-generation sequencing technology have made it easier to obtain genome sequences for various crop species, enabling the large-scale identification of DNA polymorphisms among varieties, which in turn has made DNA marker design more accessible. However, existing primer design software is not suitable for designing many types of genome-wide DNA markers from next-generation sequencing data. Here, we describe the development of V-primer, high-throughput software for designing insertion/deletion, cleaved amplified polymorphic sequence, and single-nucleotide polymorphism (SNP) markers. We validated the applicability of these markers in different crops. In addition, we performed multiplex PCR targeted amplicon sequencing using SNP markers designed with V-primer. Our results demonstrate that V-primer facilitates the efficient and accurate design of primers and is thus a useful tool for genetics, genomics, and crop breeding. V-primer is freely available at https://github.com/ncod3/vprimer.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"1 1","pages":"415-420"},"PeriodicalIF":2.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66690415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mutations within the miR172 target site of wheat <i>AP2</i> homoeologs regulate lodicule size and rachis internode length.","authors":"Agetha Bigie Nanape, Hlaing Moe Haine, Kazuhiko Sugimoto, Fuminori Kobayashi, Youko Oono, Hirokazu Handa, Takao Komatsuda, Katsuyuki Kakeda","doi":"10.1270/jsbbs.23019","DOIUrl":"10.1270/jsbbs.23019","url":null,"abstract":"<p><p>Closed fertilization in flowers, or cleistogamy, reduces the risk of fungal infection in Triticeae crops. In barley (<i>Hordeum vulgare</i>), cleistogamy is determined by a single recessive gene, <i>cly1</i>, which results from a single nucleotide polymorphism within the microRNA172 target site of the <i>Apetala2</i> (<i>AP2</i>) transcription factor gene. The recessive <i>cly1</i> allele negatively regulates the development of lodicules, keeping florets closed at anthesis. However, cleistogamy is not evident in hexaploid wheat (<i>Triticum aestivum</i>) cultivars. This study aimed at identifying mutations in wheat <i>AP2</i> orthologs by ethyl methane sulfonate-induced mutagenesis and high-resolution melt analysis. Although flowers of <i>AP2</i> mutants induced in the A and D genomes opened at anthesis, their lodicule size was significantly smaller, especially in the direction of depth, than that of wild-type plants. One of the mutants that carried a nucleotide replacement in <i>AP2</i> from the D genome produced a compact spike caused by a substantial decrease in rachis internode length, analogous to the barley dense spike. Cleistogamous hexaploid wheat might be generated by combining effective mutant alleles of <i>AP2</i>-homoeologous genes.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"1 1","pages":"401-407"},"PeriodicalIF":2.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66690466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Wild and cultivated allele effects on rice phenotypic traits in reciprocal backcross populations between <i>Oryza rufipogon</i> and two cultivars, <i>O. sativa</i> Nipponbare and IR36.","authors":"Phuong Dang Thai Phan, Akinori Nishimura, Chika Yamamoto, Pham Thien Thanh, Toshihiro Niwa, Yaddehige Priya Jayantha Amarasinghe, Ryo Ishikawa, Takashige Ishii","doi":"10.1270/jsbbs.22095","DOIUrl":"10.1270/jsbbs.22095","url":null,"abstract":"<p><p>A total of four populations of reciprocal backcross recombinant inbred lines were produced from a cross between a wild accession of <i>Oryza rufipogon</i> W630 and two major cultivars, <i>O. sativa</i> Japonica Nipponbare and Indica IR36. Using these populations, quantitative trait locus (QTL) analysis for eight morphological traits (culm length, panicle length, days to heading, panicle shape, pericarp color, hull color, seed shattering and seed awning) was carried out, and the putative QTL regions were compared among the populations. The QTLs with strong allele effects were commonly detected for culm length, panicle shape, pericarp color and hull color in all four populations, and their peak locations were close to the major genes of <i>sd1</i>, <i>Spr3</i>, <i>Rc</i> and <i>Bh4</i>, respectively. For panicle length and days to heading, some QTL regions overlapped between two or three populations. In the case of seed shattering and seed awning, strong wild allele effects at major loci were observed only in the populations with cultivated backgrounds. Since the wild and cultivated alleles have never been evaluated in the reciprocal genetic backgrounds, the present results provide new information on gene effects in breeding and domestication studies.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"1 1","pages":"373-381"},"PeriodicalIF":2.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66690074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Breeding SciencePub Date : 2023-09-01Epub Date: 2023-09-09DOI: 10.1270/jsbbs.23003
Zeki Kara, Osman Doğan
{"title":"Mutagenic effects of nitrogen protoxide and oryzalin on \"41 B\" and \"Fercal\" grapevine rootstocks seedlings.","authors":"Zeki Kara, Osman Doğan","doi":"10.1270/jsbbs.23003","DOIUrl":"10.1270/jsbbs.23003","url":null,"abstract":"<p><p>In this study, the mutagenic effects of different doses and exposure times of oryzalin and Nitrogen Protoxide (N<sub>2</sub>O) were tested for stimulating polyploid on 41 B and Fercal grapevine rootstocks seedlings. Ploidy changes were examined by morphological, cytological, macroscopic, and microscopic methods. Leaf thickness, chlorophyll contents, stomatal sizes, and chloroplast numbers of polyploid seedlings stimulated with mutagens increased but their stomatal densities decreased. Flow cytometry (FC) analyses were performed on 50 samples selected by morphological and microscopic preliminary determinations. In FC analyses, 1 tetraploid seedling and 4 mixoploid seedlings from Fercal offspring and 1 mixoploid seedling from 41 B offspring were verified. The nuclear DNA content of tetraploid and mixoploid seedlings were increased by 2.00 and 1.34-fold, respectively, when compared to their diploid parents. Chromosome counts in root tip samples propagated <i>in vitro</i> from the tetraploid Fercal offspring confirmed a 2-fold increase compared to the diploid parent. In polyploidy induction studies, it was deemed appropriate to use FC analysis and chromosome count together to confirm the ploidy levels of mutants. Oryzalin and N<sub>2</sub>O applications at different doses and exposure times were found to be effective for inducing polyploidy in 41 B and Fercal grapevine rootstocks.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"1 1","pages":"355-364"},"PeriodicalIF":2.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10722092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66690138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}