This review explores the application of enzyme‐mediated analysis using electro‐carbon sensors to investigate plant diversity. Precision plant genotype fingerprinting (PPGF) represents a paradigm shift in agricultural science, merging the fields of phyto‐enzyme identification and quantification with cutting‐edge electro‐sensor technology. PPGF acts as a powerful tool for dissecting the genetic makeup of plant species by meticulously examining their unique phyto‐enzyme signatures. Electro‐sensor technology emerges as a pioneering force, utilizing electro‐analytical methods to precisely measure and differentiate these markers. Enzyme‐based sensors are capable of detecting plant metabolites even at low concentrations, enabling highly precise and accurate measurements. Furthermore, they are generally more eco‐friendly because they use fewer hazardous chemicals and produce less waste. These sensors can function under gentle conditions and can be miniaturized, making them highly suitable for field applications. This synergistic approach between PPGF and electro‐sensor technology ushers in a transformative era, offering unprecedented insights into plant genomics and paving the way for novel avenues for PPGF. Overall, enzyme‐based electrochemical sensors contribute to improving the efficiency and effectiveness of plant fingerprinting, thereby facilitating more comprehensive and precise plant phenotyping and research endeavours.
{"title":"Exploring Plant Diversity Through Enzyme‐Mediated Analysis Using Electro‐Carbon Sensors","authors":"Vinaykumar Rachappanavar","doi":"10.1111/pbr.13223","DOIUrl":"https://doi.org/10.1111/pbr.13223","url":null,"abstract":"This review explores the application of enzyme‐mediated analysis using electro‐carbon sensors to investigate plant diversity. Precision plant genotype fingerprinting (PPGF) represents a paradigm shift in agricultural science, merging the fields of phyto‐enzyme identification and quantification with cutting‐edge electro‐sensor technology. PPGF acts as a powerful tool for dissecting the genetic makeup of plant species by meticulously examining their unique phyto‐enzyme signatures. Electro‐sensor technology emerges as a pioneering force, utilizing electro‐analytical methods to precisely measure and differentiate these markers. Enzyme‐based sensors are capable of detecting plant metabolites even at low concentrations, enabling highly precise and accurate measurements. Furthermore, they are generally more eco‐friendly because they use fewer hazardous chemicals and produce less waste. These sensors can function under gentle conditions and can be miniaturized, making them highly suitable for field applications. This synergistic approach between PPGF and electro‐sensor technology ushers in a transformative era, offering unprecedented insights into plant genomics and paving the way for novel avenues for PPGF. Overall, enzyme‐based electrochemical sensors contribute to improving the efficiency and effectiveness of plant fingerprinting, thereby facilitating more comprehensive and precise plant phenotyping and research endeavours.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"20 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Theresa Makawa Phiri, Haizheng Xiong, Yong‐Bao Pan, Ryan William Dickson, Neelendra Joshi, Alejandro Rojas, Ainong Shi
Sugarcane (Saccharum spp. hybrids) are complex polyploid and aneuploid interspecific hybrids with 110–130 chromosomes. A traditional sugarcane breeding cycle takes 13–15 years and involves multiple years and locations testing of yield. To identify molecular markers associated with yield‐related traits, the LCP 85‐384 cultivar and its mapping population of 263 self‐progenies were planted in two randomly replicated field plots. The mapping population was genotyped with amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR) and target region amplification polymorphism (TRAP) markers. Data on plant height, stalk number, stalk diameter and stalk weight were collected. A large variation was observed for each trait. A genome‐wide association study (GWAS) was conducted using mixed linear model (MLM), generalized linear model (GLM) and single marker regression (SMR) programmes of TASSEL 5 and FarmCPU of GAPIT 3. A total of 64 yield trait‐associated alleles were identified, including 11 for stalk number, 36 for stalk weight, 21 for stalk diameter and 5 for plant height. Of the 64 alleles, seven were linked to two traits and one to three traits. Genomic prediction (GP) was also performed by cross‐prediction with five models, namely, ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL). Prediction accuracy (r value) reached 0.40 for plant height, 0.36 for stalk number, 0.44 for stalk diameter and 0.54 for stalk weight with the standard errors from 0.009 to 0.012. Once verified, these markers will be a valuable tool to aid in the selection of yield‐related traits in sugarcane improvement programmes.
{"title":"Genomic Association and Prediction Study for Yield Traits in a Sugarcane (Saccharum spp. Hybrids) Mapping Population ‘LCP 85‐384’","authors":"Theresa Makawa Phiri, Haizheng Xiong, Yong‐Bao Pan, Ryan William Dickson, Neelendra Joshi, Alejandro Rojas, Ainong Shi","doi":"10.1111/pbr.13221","DOIUrl":"https://doi.org/10.1111/pbr.13221","url":null,"abstract":"Sugarcane (<jats:italic>Saccharum</jats:italic> spp. hybrids) are complex polyploid and aneuploid interspecific hybrids with 110–130 chromosomes. A traditional sugarcane breeding cycle takes 13–15 years and involves multiple years and locations testing of yield. To identify molecular markers associated with yield‐related traits, the LCP 85‐384 cultivar and its mapping population of 263 self‐progenies were planted in two randomly replicated field plots. The mapping population was genotyped with amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR) and target region amplification polymorphism (TRAP) markers. Data on plant height, stalk number, stalk diameter and stalk weight were collected. A large variation was observed for each trait. A genome‐wide association study (GWAS) was conducted using mixed linear model (MLM), generalized linear model (GLM) and single marker regression (SMR) programmes of TASSEL 5 and FarmCPU of GAPIT 3. A total of 64 yield trait‐associated alleles were identified, including 11 for stalk number, 36 for stalk weight, 21 for stalk diameter and 5 for plant height. Of the 64 alleles, seven were linked to two traits and one to three traits. Genomic prediction (GP) was also performed by cross‐prediction with five models, namely, ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL). Prediction accuracy (<jats:italic>r</jats:italic> value) reached 0.40 for plant height, 0.36 for stalk number, 0.44 for stalk diameter and 0.54 for stalk weight with the standard errors from 0.009 to 0.012. Once verified, these markers will be a valuable tool to aid in the selection of yield‐related traits in sugarcane improvement programmes.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"4 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Satvinder Singh, Anju Arora, Karthick S. Babu, S. K. Verma, R. K. Panwar, Meena Agnihotri
The leguminous chickpea is a good source of protein, but its yield potential is frequently constrained by biotic stresses, primarily Helicoverpa armigera, a major havoc for cultivation of the crop. To develop host plant resistance for minimizing the losses due to the pod borer, five kabuli parents with desired traits for pod borer tolerance were crossed in diallel mating design to produce 10 crosses which were analysed for traits related to pod borer and nutrition. Based on correlation studies, trichome density was found positively correlated with phenol content, but both the traits were negatively associated with number of damaged seeds. Therefore, the tolerant genotypes were identified on the basis of phenol content, trichome density, number of damaged seeds and field rating. Among parents ICC 12197 was found superior in terms of yield and borer tolerance features with an intermediate pest resistance susceptible rating in addition to higher Fe content. However, significant sca effects for higher phenol content and seed yield in ICC 11764 × ICC 14190 were recorded with reduced number of damaged seeds in addition to higher Fe and Zn content. It was observed that the specific combination involved good and poor combiners for each trait. The same cross also showed significant standard heterosis in desirable direction for phenol content, trichome density, number of damaged seeds and seed yield. Additionally, the ratio of σ2 GCA to σ2 SCA revealed nonadditive gene action in controlling the expression of phenol content, trichome density, number of damaged seeds and Fe and Zn content. Thus, breeder may focus efforts on desirable cross utilizing selection in further segregating generations for higher phenol content, trichome density and Fe and Zn content in addition to yield‐related traits while lesser number of damaged seeds per plant to concentrate for development of pod borer resilient high yielding kabuli genotypes to combat micronutrient deficiency.
{"title":"Integrating Antixenosis Against Helicoverpa armigera (Lepidoptera: Noctuidae) and Micronutrition in Kabuli Chickpea (Cicer arietinum L.) Genotypes","authors":"Satvinder Singh, Anju Arora, Karthick S. Babu, S. K. Verma, R. K. Panwar, Meena Agnihotri","doi":"10.1111/pbr.13218","DOIUrl":"https://doi.org/10.1111/pbr.13218","url":null,"abstract":"The leguminous chickpea is a good source of protein, but its yield potential is frequently constrained by biotic stresses, primarily <jats:italic>Helicoverpa armigera</jats:italic>, a major havoc for cultivation of the crop. To develop host plant resistance for minimizing the losses due to the pod borer, five <jats:italic>kabuli</jats:italic> parents with desired traits for pod borer tolerance were crossed in diallel mating design to produce 10 crosses which were analysed for traits related to pod borer and nutrition. Based on correlation studies, trichome density was found positively correlated with phenol content, but both the traits were negatively associated with number of damaged seeds. Therefore, the tolerant genotypes were identified on the basis of phenol content, trichome density, number of damaged seeds and field rating. Among parents ICC 12197 was found superior in terms of yield and borer tolerance features with an intermediate pest resistance susceptible rating in addition to higher Fe content. However, significant <jats:italic>sca</jats:italic> effects for higher phenol content and seed yield in ICC 11764 × ICC 14190 were recorded with reduced number of damaged seeds in addition to higher Fe and Zn content. It was observed that the specific combination involved good and poor combiners for each trait. The same cross also showed significant standard heterosis in desirable direction for phenol content, trichome density, number of damaged seeds and seed yield. Additionally, the ratio of <jats:italic>σ</jats:italic><jats:sup>2</jats:sup> GCA to <jats:italic>σ</jats:italic><jats:sup>2</jats:sup> SCA revealed nonadditive gene action in controlling the expression of phenol content, trichome density, number of damaged seeds and Fe and Zn content. Thus, breeder may focus efforts on desirable cross utilizing selection in further segregating generations for higher phenol content, trichome density and Fe and Zn content in addition to yield‐related traits while lesser number of damaged seeds per plant to concentrate for development of pod borer resilient high yielding <jats:italic>kabuli</jats:italic> genotypes to combat micronutrient deficiency.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"37 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Johannes Schneider, Katherine Frels, Sandeep Sakhale, P. Stephen Baenziger, C. Friedrich H. Longin, Jochen C. Reif, Albert W. Schulthess
Hybrid wheat could deliver the grain yield (GY) and stability levels to confront climate change while crossing genetically divergent pools should maximize heterosis. We crossed 22 breeding lines from Nebraska (USA) with two German cultivars to produce 44 hybrids. Hybrids, parents and 12 checks were reciprocally tested across their contrasting target environments for GY, plant height and flowering biology during 2 consecutive years at multiple locations. Trait variation within target environments had the greatest impact on performance. Therefore, mega‐environments could not be derived from target environments despite a clear clustering using weather variables. Short plants and locally optimized flowering biology were main drivers for crop performance and adaptation. Modified Rogers' distances derived from genotyping‐by‐sequencing revealed the genetic divergence between German and ‘Great Plains’ pools. However, variation on GY heterosis could not be explained by this divergence. In general, GY of hybrids was more stable across target environments than for locally adapted material, whereas GY heterosis was higher under harsh climate conditions of the Nebraska's ‘Great Plains’.
{"title":"Reciprocal Evaluation of Hybrid Wheat (Triticum aestivum L.) Crosses Between German and US ‘Great Plains’ Genotypes Across Their Contrasting Target Environments","authors":"Johannes Schneider, Katherine Frels, Sandeep Sakhale, P. Stephen Baenziger, C. Friedrich H. Longin, Jochen C. Reif, Albert W. Schulthess","doi":"10.1111/pbr.13220","DOIUrl":"https://doi.org/10.1111/pbr.13220","url":null,"abstract":"Hybrid wheat could deliver the grain yield (GY) and stability levels to confront climate change while crossing genetically divergent pools should maximize heterosis. We crossed 22 breeding lines from Nebraska (USA) with two German cultivars to produce 44 hybrids. Hybrids, parents and 12 checks were reciprocally tested across their contrasting target environments for GY, plant height and flowering biology during 2 consecutive years at multiple locations. Trait variation within target environments had the greatest impact on performance. Therefore, mega‐environments could not be derived from target environments despite a clear clustering using weather variables. Short plants and locally optimized flowering biology were main drivers for crop performance and adaptation. Modified Rogers' distances derived from genotyping‐by‐sequencing revealed the genetic divergence between German and ‘Great Plains’ pools. However, variation on GY heterosis could not be explained by this divergence. In general, GY of hybrids was more stable across target environments than for locally adapted material, whereas GY heterosis was higher under harsh climate conditions of the Nebraska's ‘Great Plains’.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"71 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cotton–melon aphid (Aphis gossypii) is a highly destructive pest that causes serious yield losses in cucumber production. IL52, a Cucumis hystrix introgression line of cucumber, exhibits resistance to a number of diseases and also shows strong resistance to aphids. To characterize the type of aphid resistance in IL52, we designed a separate leaf‐disc/no‐choice test and free‐choice test to examine antibiosis and antixenosis, respectively. Our results indicated that IL52 displayed antixenosis resistance to aphids. In other words, when planted with other lines such as CCMC, IL52 was not favourable to aphids. To dissect the genetic basis of antixenosis resistance in IL52, we evaluated a mapping population of 155 lines from CCMC × IL52–derived F7:8 RIL using free‐choice test for aphid resistance. A major‐effect QTL on Chr2, designated as qRag2.1 (Resistant to A. gossypii), was identified as being significantly associated with aphid resistance. The QTL qRag2.1 was mapped to an interval flanked by markers UW085197 and SSR11909, spanning a physical location of 15.14–19.07 Mb, which explained 12.74%–14.03% of the phenotypic variance. Analysis of polymorphisms between the parental lines using resequencing data revealed one gene, CsaV3_2G018180, with three nonsynonymous amino acid substitutions and a 6‐bp InDel in its coding sequence (CDS). CsaV3_2G018180 encodes a pectinesterase/pectinesterase inhibitor enzyme, designated as CsPEI, which has been reported to regulate pectin methylesterase activity that is implicated in various biological processes. The relative expression level of CsPEI was induced in IL52 post aphid infestation, suggesting it could be a potential candidate gene for aphid resistance.
{"title":"Characterization and Genetic Mapping of Resistance to Cotton–Melon Aphid (Aphis gossypii) in Cucumber","authors":"Shixiong Ning, Lei Xia, Yu Fang, Zhengyue Zhou, Yuhui Wang, Jinfeng Chen","doi":"10.1111/pbr.13213","DOIUrl":"https://doi.org/10.1111/pbr.13213","url":null,"abstract":"Cotton–melon aphid (<jats:styled-content style=\"fixed-case\"><jats:italic>Aphis gossypii</jats:italic></jats:styled-content>) is a highly destructive pest that causes serious yield losses in cucumber production. IL52, a <jats:italic>Cucumis hystrix</jats:italic> introgression line of cucumber, exhibits resistance to a number of diseases and also shows strong resistance to aphids. To characterize the type of aphid resistance in IL52, we designed a separate leaf‐disc/no‐choice test and free‐choice test to examine antibiosis and antixenosis, respectively. Our results indicated that IL52 displayed antixenosis resistance to aphids. In other words, when planted with other lines such as CCMC, IL52 was not favourable to aphids. To dissect the genetic basis of antixenosis resistance in IL52, we evaluated a mapping population of 155 lines from CCMC × IL52–derived F<jats:sub>7:8</jats:sub> RIL using free‐choice test for aphid resistance. A major‐effect QTL on Chr2, designated as <jats:italic>qRag2.1</jats:italic> (<jats:italic>Resistant to <jats:styled-content style=\"fixed-case\">A. gossypii</jats:styled-content></jats:italic>), was identified as being significantly associated with aphid resistance. The QTL <jats:italic>qRag2.1</jats:italic> was mapped to an interval flanked by markers UW085197 and SSR11909, spanning a physical location of 15.14–19.07 Mb, which explained 12.74%–14.03% of the phenotypic variance. Analysis of polymorphisms between the parental lines using resequencing data revealed one gene, <jats:italic>CsaV3_2G018180</jats:italic>, with three nonsynonymous amino acid substitutions and a 6‐bp InDel in its coding sequence (CDS). <jats:italic>CsaV3_2G018180</jats:italic> encodes a pectinesterase/pectinesterase inhibitor enzyme, designated as <jats:italic>CsPEI</jats:italic>, which has been reported to regulate pectin methylesterase activity that is implicated in various biological processes. The relative expression level of <jats:italic>CsPEI</jats:italic> was induced in IL52 post aphid infestation, suggesting it could be a potential candidate gene for aphid resistance.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"50 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The partially waxy wheat with single and double deletion of Wx gene have desirable texture in noodles. The selecting of partially waxy wheat with strong gluten has become one of the main targets in the breeding of high‐quality wheat for noodles. This study aimed to explore a method for identifying fully waxy or partially waxy wheat with different Wx gene deletion by using pasting properties. In this study, the viscosity ratio (VR) index was brought forward for the first time. The impacts of the eight allelic types with different Wx genes on pasting parameters were studied by using 60 double haploid (DH) lines from the same combination (Experiment I), and 85 samples consisted of main varieties and a few advanced lines from the Huanghuai wheat region (Experiment II). The results revealed the viscosity ratio was significantly different among allelic deletion types. More surprisingly, the wild type, three single deletion types, three double deletion types and full waxy type among the eight alleles, respectively, exhibited distinct distribution intervals for viscosity ratios, enabling the preliminary determination of specific Wx gene deletion types based on VR. Therefore, the VR value can serve as an effective index for identifying fully and partially waxy wheat lines during breeding selection, and it holds significant potential in the breeding of high‐quality wheat for noodles.
{"title":"Identification of Full or Partially Waxy Wheat by Using Viscosity Ratio Index","authors":"Xiangcun Zan, Yingying Chang, Yongxia Wang, Yumin Wang, Haibin Dong, Xueli Qi","doi":"10.1111/pbr.13222","DOIUrl":"https://doi.org/10.1111/pbr.13222","url":null,"abstract":"The partially waxy wheat with single and double deletion of Wx gene have desirable texture in noodles. The selecting of partially waxy wheat with strong gluten has become one of the main targets in the breeding of high‐quality wheat for noodles. This study aimed to explore a method for identifying fully waxy or partially waxy wheat with different Wx gene deletion by using pasting properties. In this study, the viscosity ratio (VR) index was brought forward for the first time. The impacts of the eight allelic types with different Wx genes on pasting parameters were studied by using 60 double haploid (DH) lines from the same combination (Experiment I), and 85 samples consisted of main varieties and a few advanced lines from the Huanghuai wheat region (Experiment II). The results revealed the viscosity ratio was significantly different among allelic deletion types. More surprisingly, the wild type, three single deletion types, three double deletion types and full waxy type among the eight alleles, respectively, exhibited distinct distribution intervals for viscosity ratios, enabling the preliminary determination of specific Wx gene deletion types based on VR. Therefore, the VR value can serve as an effective index for identifying fully and partially waxy wheat lines during breeding selection, and it holds significant potential in the breeding of high‐quality wheat for noodles.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"21 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kunyan Zou, Minjae Choi, Jeong‐Dong Lee, Kyung Do Kim, Hyeon Do Lim, Ki‐Seung Kim, Tae‐Hwan Jun
Investigating the inheritance and genetic variation of luteolin content in peanut shells is pivotal for developing improved cultivars with high luteolin content. In this study, we developed a genetic map spanning 976.8 cM using 115 highly advanced recombinant inbred lines (RILs) and the Axiom_Arachis array containing 58K single‐nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) analysis was then performed using phenotype data from 2‐year field trials. From these analyses, we identified three significant QTLs with 4.1%–11.7% phenotypic variation explained (PVE) for luteolin content in peanut shells. We further identified five candidate genes with putative functions suggesting possible involvement in plant flavonoid and terpenoid biosynthetic pathways in peanut luteolin biosynthesis. Additionally, two new peanut inbreeding lines with high luteolin and oleic acid levels were selected and are expected to be used as multifunctional genomic backgrounds for future breeding and research programs. The information on the QTL regions and candidate genes from the present study could be very useful for developing new peanut cultivars with high luteolin content and for identifying the genetic/genomic determinants of luteolin content in peanut shells.
{"title":"Identification of QTL Associated With Luteolin Content in Peanut (Arachis hypogaea L.) Shells","authors":"Kunyan Zou, Minjae Choi, Jeong‐Dong Lee, Kyung Do Kim, Hyeon Do Lim, Ki‐Seung Kim, Tae‐Hwan Jun","doi":"10.1111/pbr.13216","DOIUrl":"https://doi.org/10.1111/pbr.13216","url":null,"abstract":"Investigating the inheritance and genetic variation of luteolin content in peanut shells is pivotal for developing improved cultivars with high luteolin content. In this study, we developed a genetic map spanning 976.8 cM using 115 highly advanced recombinant inbred lines (RILs) and the Axiom_Arachis array containing 58K single‐nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) analysis was then performed using phenotype data from 2‐year field trials. From these analyses, we identified three significant QTLs with 4.1%–11.7% phenotypic variation explained (PVE) for luteolin content in peanut shells. We further identified five candidate genes with putative functions suggesting possible involvement in plant flavonoid and terpenoid biosynthetic pathways in peanut luteolin biosynthesis. Additionally, two new peanut inbreeding lines with high luteolin and oleic acid levels were selected and are expected to be used as multifunctional genomic backgrounds for future breeding and research programs. The information on the QTL regions and candidate genes from the present study could be very useful for developing new peanut cultivars with high luteolin content and for identifying the genetic/genomic determinants of luteolin content in peanut shells.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"100 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sajid Shokat, Mian Abdur Rehman Arif, Bruno Trevenzoli Favero, Pooja Bhatnagar‐Mathur, Marta S. Lopes, Fulai Liu, Sukhwinder Singh
This study employed genome‐wide association studies (GWAS) to identify the crucial marker–trait associations (MTAs) for agronomic and physiological traits in bread wheat grown under full irrigation and 40% reduced irrigation. One hundred twenty‐four genotypes derived from three‐way crosses of landraces and synthetic bread wheat were evaluated for 2 years in the field conditions of CIMMYT Obregon, Mexico. Irrigation was not provided at anthesis and post‐anthesis stage for the drought treatment, and data of 12 traits were recorded. Most of the traits were reduced significantly under drought conditions except for vigour, wax and spike length (SL); genotypes were significantly different for the eight traits except for days to heading (DTH), number of grains spike−1 (NGS), normalized difference in vegetation index (NDVI) and canopy temperature depression (CTD); and differences were also significant for five traits between the years. Moreover, GY was significantly and negatively correlated with wax and CTD. Our GWAS results indicated 117 significant (p ≤ 0.001) MTAs distributed on all the wheat chromosomes except chromosomes 4B and 4D explaining 10%–21.5% of the phenotypic variation of the corresponding traits. Moreover, 22 MTAs were recorded for grain yield and explaining the phenotypic variations up to 14.7% with one common association under both irrigated and drought conditions. Additionally, we also identified the associations for NDVI, CTD and SL at chromosome 1B, suggesting that genotypes are sustaining superior grain yield through better values of traits like NDVI, CTD, and SL under the challenging conditions of anthesis and post‐anthesis drought stress.
{"title":"Genome‐Wide Association Studies Predicted Drought Stress Occuring at Anthesis and Post‐Anthesis Stages in Novel Diverse Germplasm of Bread Wheat (Triticum aestivum)","authors":"Sajid Shokat, Mian Abdur Rehman Arif, Bruno Trevenzoli Favero, Pooja Bhatnagar‐Mathur, Marta S. Lopes, Fulai Liu, Sukhwinder Singh","doi":"10.1111/pbr.13219","DOIUrl":"https://doi.org/10.1111/pbr.13219","url":null,"abstract":"This study employed genome‐wide association studies (GWAS) to identify the crucial marker–trait associations (MTAs) for agronomic and physiological traits in bread wheat grown under full irrigation and 40% reduced irrigation. One hundred twenty‐four genotypes derived from three‐way crosses of landraces and synthetic bread wheat were evaluated for 2 years in the field conditions of CIMMYT Obregon, Mexico. Irrigation was not provided at anthesis and post‐anthesis stage for the drought treatment, and data of 12 traits were recorded. Most of the traits were reduced significantly under drought conditions except for vigour, wax and spike length (SL); genotypes were significantly different for the eight traits except for days to heading (DTH), number of grains spike<jats:sup>−1</jats:sup> (NGS), normalized difference in vegetation index (NDVI) and canopy temperature depression (CTD); and differences were also significant for five traits between the years. Moreover, GY was significantly and negatively correlated with wax and CTD. Our GWAS results indicated 117 significant (<jats:italic>p</jats:italic> ≤ 0.001) MTAs distributed on all the wheat chromosomes except chromosomes 4B and 4D explaining 10%–21.5% of the phenotypic variation of the corresponding traits. Moreover, 22 MTAs were recorded for grain yield and explaining the phenotypic variations up to 14.7% with one common association under both irrigated and drought conditions. Additionally, we also identified the associations for NDVI, CTD and SL at chromosome 1B, suggesting that genotypes are sustaining superior grain yield through better values of traits like NDVI, CTD, and SL under the challenging conditions of anthesis and post‐anthesis drought stress.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"57 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yuhong Li, Wei Shi, Shuhao Zhu, Ling Yu, Yue Cai, Zhiping Wang, Jianju Liu, Yunyu Wu, Cunhong Pan, Zichun Chen, Changhai Zhou, Hongjuan Ji, Niansheng Huang, Xiaoxiang Zhang, Peng Gao, Jun Jiao, Ning Xiao, Aihong Li
Tiller number and effective panicle number are important factors affecting rice yield. In this study, the sequencing data of 331 rice varieties were used to carry out genome‐wide association study (GWAS) of these two factors. A total of 58 candidate genes related to tiller number were identified, and their functions involved energy metabolism and cytoplasmic membrane metabolism pathways. There were 19 candidate genes related to effective panicle number, whose functions involved energy metabolism, cytoplasmic membrane metabolism and signal transduction pathways. A new QTL ‘qTNP12’, which controls both tiller number and effective panicle number, was identified on chromosome 12. There was specific variation in the 275th amino acid in the coding frame of the candidate gene. Indica rice with multiple tillers had histidine variation, while japonica rice with few tillers and Oryza rufipogon had arginine variation. Evolutionary analysis showed that the multi‐tiller trait of indica rice was developed through artificial selection and domestication. The results of this study provide a foundation for further clarifying the molecular mechanism of qTPN12 regulating tiller and effective panicle, as well as improving rice architecture through molecular marker‐assisted selection.
{"title":"Genome‐Wide Association Study Reveals Candidate Genes Controlling Tillering and Effective Panicle Number in Rice (Oryza sativa L.)","authors":"Yuhong Li, Wei Shi, Shuhao Zhu, Ling Yu, Yue Cai, Zhiping Wang, Jianju Liu, Yunyu Wu, Cunhong Pan, Zichun Chen, Changhai Zhou, Hongjuan Ji, Niansheng Huang, Xiaoxiang Zhang, Peng Gao, Jun Jiao, Ning Xiao, Aihong Li","doi":"10.1111/pbr.13215","DOIUrl":"https://doi.org/10.1111/pbr.13215","url":null,"abstract":"Tiller number and effective panicle number are important factors affecting rice yield. In this study, the sequencing data of 331 rice varieties were used to carry out genome‐wide association study (GWAS) of these two factors. A total of 58 candidate genes related to tiller number were identified, and their functions involved energy metabolism and cytoplasmic membrane metabolism pathways. There were 19 candidate genes related to effective panicle number, whose functions involved energy metabolism, cytoplasmic membrane metabolism and signal transduction pathways. A new QTL ‘<jats:italic>qTNP12</jats:italic>’, which controls both tiller number and effective panicle number, was identified on chromosome 12. There was specific variation in the 275th amino acid in the coding frame of the candidate gene. Indica rice with multiple tillers had histidine variation, while japonica rice with few tillers and <jats:styled-content style=\"fixed-case\"><jats:italic>Oryza rufipogon</jats:italic></jats:styled-content> had arginine variation. Evolutionary analysis showed that the multi‐tiller trait of indica rice was developed through artificial selection and domestication. The results of this study provide a foundation for further clarifying the molecular mechanism of <jats:italic>qTPN12</jats:italic> regulating tiller and effective panicle, as well as improving rice architecture through molecular marker‐assisted selection.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"76 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joseph Jensen, Hannah Uhlmann, Jennifer Lachowiec, Greg Lutgen, Jason P. Cook, Xiang S. Yin, Ken Kephart, Jamie Sherman
Dormancy in barley has been thoroughly studied and shown to negatively impact malt quality, resulting in selection against dormancy. However, reduced dormancy coincides with increased preharvest sprout (PHS) risk, thus sparking a new interest in integrating dormancy back into American barley lines if the negative effects of dormancy on malt quality can be overcome. We evaluated the dormancy and hydration index (HYI) in a biparental mapping population to determine the genotypes that would protect against PHS but have good malt quality. We found 4 HYI QTLs and 4 dormancy QTLs, one of which was near the well‐described SD2 QTL. The HYI QTLs were pleiotropically related to seed size (1H), dormancy (5H) and malt quality (2H). Lines with dormancy (5H) and increased HYI (2H and 3H) had malt quality similar to nondormant lines while maintaining PHS resistance, suggesting improvements in HYI could be the key to overcoming the negative effects of dormancy in malting.
{"title":"Improvement of Endosperm Hydration Counter the Negative Relationship Between Dormancy and Malt Quality in Barley (Hordeum vulgare)","authors":"Joseph Jensen, Hannah Uhlmann, Jennifer Lachowiec, Greg Lutgen, Jason P. Cook, Xiang S. Yin, Ken Kephart, Jamie Sherman","doi":"10.1111/pbr.13217","DOIUrl":"https://doi.org/10.1111/pbr.13217","url":null,"abstract":"Dormancy in barley has been thoroughly studied and shown to negatively impact malt quality, resulting in selection against dormancy. However, reduced dormancy coincides with increased preharvest sprout (PHS) risk, thus sparking a new interest in integrating dormancy back into American barley lines if the negative effects of dormancy on malt quality can be overcome. We evaluated the dormancy and hydration index (HYI) in a biparental mapping population to determine the genotypes that would protect against PHS but have good malt quality. We found 4 HYI QTLs and 4 dormancy QTLs, one of which was near the well‐described SD2 QTL. The HYI QTLs were pleiotropically related to seed size (1H), dormancy (5H) and malt quality (2H). Lines with dormancy (5H) and increased HYI (2H and 3H) had malt quality similar to nondormant lines while maintaining PHS resistance, suggesting improvements in HYI could be the key to overcoming the negative effects of dormancy in malting.","PeriodicalId":20228,"journal":{"name":"Plant Breeding","volume":"106 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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