Pub Date : 2023-03-24DOI: 10.1017/s1479262123000163
A. F. das Neves, C. A. Mangolin, V. N. A. Fernandes, E. R. Monteiro, M. F. Machado
Although morphological plasticity has been widely known in various cactus genera, few studies have investigated the origin and molecular relationship between morphological variants from cacti. Morphological variants are relevant specimens because atypical, exotic and generally unique forms are preferred by cactus traders and collectors. The current study investigates the molecular relationship between the tortuosus and monstruosus ornamental variants of Cereus peruvianus used in landscapes. Polymorphisms in loci of simple-sequence repeats in DNA were used as molecular markers. The variants tortuosus and monstruosus, and plants with typically columnar and erect shoots cultivated in southern Brazil were retrieved from public parks and home gardens. High polymorphism, an indicative of vegetative propagation, and a moderate genetic divergence were detected at the molecular level in monstruosus and tortuosus plants. Artificial selection and vegetative propagation of the ornamental variants of Cereus may be inducing a moderate genetic divergence and formation of two heterologous groups with conservative genetic diversity. Polymorphism in Cereus variants revealed groups with contrasting genes among the variants tortuosus and monstruosus which may be useful for breeding to generate new and different new variants.
{"title":"Morphological and molecular divergence in ornamental variants of cactus which may be useful to generate new variants","authors":"A. F. das Neves, C. A. Mangolin, V. N. A. Fernandes, E. R. Monteiro, M. F. Machado","doi":"10.1017/s1479262123000163","DOIUrl":"https://doi.org/10.1017/s1479262123000163","url":null,"abstract":"\u0000 Although morphological plasticity has been widely known in various cactus genera, few studies have investigated the origin and molecular relationship between morphological variants from cacti. Morphological variants are relevant specimens because atypical, exotic and generally unique forms are preferred by cactus traders and collectors. The current study investigates the molecular relationship between the tortuosus and monstruosus ornamental variants of Cereus peruvianus used in landscapes. Polymorphisms in loci of simple-sequence repeats in DNA were used as molecular markers. The variants tortuosus and monstruosus, and plants with typically columnar and erect shoots cultivated in southern Brazil were retrieved from public parks and home gardens. High polymorphism, an indicative of vegetative propagation, and a moderate genetic divergence were detected at the molecular level in monstruosus and tortuosus plants. Artificial selection and vegetative propagation of the ornamental variants of Cereus may be inducing a moderate genetic divergence and formation of two heterologous groups with conservative genetic diversity. Polymorphism in Cereus variants revealed groups with contrasting genes among the variants tortuosus and monstruosus which may be useful for breeding to generate new and different new variants.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"118 11-12","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72448961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-22DOI: 10.1017/s147926212300014x
M. Girija Rani, P. Satyanarayana, N. Chamundeswari, P. V. R. Ramana Rao, M. Prabhakar, B. Ravikumar, P. Nagakumari, K. Kalpana
Rice crop is affected by different types of floods at different stages of the crop cycle. Constant efforts of researchers resulted in the development of rice varieties for anaerobic germination, flash floods and stagnant flooding by both conventional and molecular breeding approaches. Detection of QTLs for different types of floods in new genetic source (AC39416A) is needed to combat adverse effects of climate change. Present investigation was carried out to identify QTLs for flood tolerance using recombinant inbred lines derived from Indra and AC39416A. QTL mapping resulted in identification of QTLs, qAG3.1 on chromosome 3 for anaerobic germination and qSF10.1 on chromosome 10 for plant survival % under stagnant flooding. These QTLs explain 59.08 and 13.21% of phenotypic variance respectively. Two candidate genes were identified in qAG3.1 region, LOC_Os03g42130 gibberellin 20 oxidase2 and LOC_Os03g44170 glutathione S-transferase. The underlying mechanism might be the inhibition of gibberellic acid synthesis and thereby protecting seedlings from oxidative stress under anoxia condition. Genomic region of qSF10.1 revealed LOC_Os10g35020 glycosyltransferase and LOC_Os10g35050 aquaporin protein loci, which might be responsible for adaptive mechanism for plant survival % under stagnant flooding. This indicates that the new genetic resource AC39416A has an ability to adopt to different types of flood tolerance in response to environmental stress. Unveiling physiological and molecular mechanisms for flood tolerance in AC39416A using advanced omics studies would help in precise genomic selections for sustained production in flood-prone areas.
{"title":"Mapping of QTLs for flood tolerance in rice using recombinant inbred lines of Indra and a new plant genetic resource AC 39416 A","authors":"M. Girija Rani, P. Satyanarayana, N. Chamundeswari, P. V. R. Ramana Rao, M. Prabhakar, B. Ravikumar, P. Nagakumari, K. Kalpana","doi":"10.1017/s147926212300014x","DOIUrl":"https://doi.org/10.1017/s147926212300014x","url":null,"abstract":"\u0000 Rice crop is affected by different types of floods at different stages of the crop cycle. Constant efforts of researchers resulted in the development of rice varieties for anaerobic germination, flash floods and stagnant flooding by both conventional and molecular breeding approaches. Detection of QTLs for different types of floods in new genetic source (AC39416A) is needed to combat adverse effects of climate change. Present investigation was carried out to identify QTLs for flood tolerance using recombinant inbred lines derived from Indra and AC39416A. QTL mapping resulted in identification of QTLs, qAG3.1 on chromosome 3 for anaerobic germination and qSF10.1 on chromosome 10 for plant survival % under stagnant flooding. These QTLs explain 59.08 and 13.21% of phenotypic variance respectively. Two candidate genes were identified in qAG3.1 region, LOC_Os03g42130 gibberellin 20 oxidase2 and LOC_Os03g44170 glutathione S-transferase. The underlying mechanism might be the inhibition of gibberellic acid synthesis and thereby protecting seedlings from oxidative stress under anoxia condition. Genomic region of qSF10.1 revealed LOC_Os10g35020 glycosyltransferase and LOC_Os10g35050 aquaporin protein loci, which might be responsible for adaptive mechanism for plant survival % under stagnant flooding. This indicates that the new genetic resource AC39416A has an ability to adopt to different types of flood tolerance in response to environmental stress. Unveiling physiological and molecular mechanisms for flood tolerance in AC39416A using advanced omics studies would help in precise genomic selections for sustained production in flood-prone areas.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"56 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88823781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-16DOI: 10.1017/s1479262123000138
Luyao Ma, Cheng Liu, Jing Xin, Bin Li, Junrong Tang, Yaxuan Xin, P. Ye, Peiyao Xin, B. Bai
The plant Camellia fascicularis, belonging to family Theaceae, has high ornamental and medicinal value, and rare gene resources for genetic improvement of Camellia crops, but is currently threatened with extinction because of the unique and extremely small wild populations. Molecular markers have clarified the wild plant species’ genetic diversity structure, new gene resources and relationship with crops. This will be beneficial for conservation of these valuable crop-related wild species and crop improvement. In this study, we identified 95,979 microsatellite loci from 155,011 transcriptome unigenes, and developed 14 polymorphic expressed sequence tag-derived simple sequence repeat (EST-SSR) microsatellite markers for C. fascicularis. The number of alleles (Na) per locus was 2–8 with a mean of 4.86. The genetic diversity of 40 individuals from four natural populations of C. fascicularis was analysed using these polymorphic markers. The number of alleles (Na) for EST-SSR ranged from 2 to 5, with the expected heterozygosities (He) and observed heterozygosities (Ho) in all loci ranging from 0.183 to 0.683, and from 0.201 to 0.700, respectively, implying a rich genetic variation present in wild C. fascicularis populations. Moreover, the phylogenetic analysis among four populations, using the 14 EST-SSR markers developed in this study, grouped 40 individuals into three groups, which coincide with their geographic distribution. These results showed that 14 EST-SSR markers are available for the analysis of genetic variation in C. fascicularis populations and genetic improvement of new Camellias cultivars by interspecific hybridization, and are beneficial for conservation of the endangered species.
{"title":"Development of EST-SSR markers for an endangered plant species, Camellia fascicularis (Theaceae)","authors":"Luyao Ma, Cheng Liu, Jing Xin, Bin Li, Junrong Tang, Yaxuan Xin, P. Ye, Peiyao Xin, B. Bai","doi":"10.1017/s1479262123000138","DOIUrl":"https://doi.org/10.1017/s1479262123000138","url":null,"abstract":"\u0000 The plant Camellia fascicularis, belonging to family Theaceae, has high ornamental and medicinal value, and rare gene resources for genetic improvement of Camellia crops, but is currently threatened with extinction because of the unique and extremely small wild populations. Molecular markers have clarified the wild plant species’ genetic diversity structure, new gene resources and relationship with crops. This will be beneficial for conservation of these valuable crop-related wild species and crop improvement. In this study, we identified 95,979 microsatellite loci from 155,011 transcriptome unigenes, and developed 14 polymorphic expressed sequence tag-derived simple sequence repeat (EST-SSR) microsatellite markers for C. fascicularis. The number of alleles (Na) per locus was 2–8 with a mean of 4.86. The genetic diversity of 40 individuals from four natural populations of C. fascicularis was analysed using these polymorphic markers. The number of alleles (Na) for EST-SSR ranged from 2 to 5, with the expected heterozygosities (He) and observed heterozygosities (Ho) in all loci ranging from 0.183 to 0.683, and from 0.201 to 0.700, respectively, implying a rich genetic variation present in wild C. fascicularis populations. Moreover, the phylogenetic analysis among four populations, using the 14 EST-SSR markers developed in this study, grouped 40 individuals into three groups, which coincide with their geographic distribution. These results showed that 14 EST-SSR markers are available for the analysis of genetic variation in C. fascicularis populations and genetic improvement of new Camellias cultivars by interspecific hybridization, and are beneficial for conservation of the endangered species.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"23 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88986100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-09DOI: 10.1017/s1479262123000102
C. H. A. Matos-Filho, José Eduardo Vasconcelos de Carvalho-Junior, G. D. N. Costa, Marcones Ferreira Costa, J. A. R. Nunes, Â. C. D. A. Lopes, Regina Lucia Ferreira-Gomes
Cashew (Anacardium occidentale L.) is cultivated in more than 30 countries because of its economic and nutritional importance. Despite having a significant agronomic role, little is known about the genetic and phenotypic diversity of cashew populations in Brazil. Thus, we aimed to characterize and estimate the diversity among cashew genotypes based on agro-morphological and physicochemical traits, with an objective of selection of varieties for breeding programmes. Forty-three cashew trees were evaluated based on 13 morphological traits and three physicochemical traits. A wide range of variations was recorded for the phenotypic characteristics, including total weight, fruit weight, pseudofruit length, kernel weight and total acidity, suggesting the existence of considerable variations for potential use in breeding programmes. Principal component analysis explained 79.74% of the total variation in the first two principal axes. The dendrogram based on the UPGMA method classified the 43 genotypes into six groups. Groups IV and VI were the most dissimilar, with emphasis on the genotypes 28 and 43, which were observed to be most divergent based on the Euclidean distance matrix (3.054). This makes it possible to select genotypes for hybridization with F1 generation gains. Based on cluster analysis and comparison of means among the six groups, promising genotypes were identified with superior traits, such as fruit weight, pseudofruit length, kernel weight and total acidity. This suggests the importance of phenotypic characterization for cashew breeding programmes. In addition, the observed vast diversity is an important genetic basis for improving cashew yield in northeastern Brazil.
{"title":"Estimation of the extent of phenotypic diversity among cashew (Anacardium occidentale L.) genotypes based on agro-morphological and physicochemical traits","authors":"C. H. A. Matos-Filho, José Eduardo Vasconcelos de Carvalho-Junior, G. D. N. Costa, Marcones Ferreira Costa, J. A. R. Nunes, Â. C. D. A. Lopes, Regina Lucia Ferreira-Gomes","doi":"10.1017/s1479262123000102","DOIUrl":"https://doi.org/10.1017/s1479262123000102","url":null,"abstract":"\u0000 Cashew (Anacardium occidentale L.) is cultivated in more than 30 countries because of its economic and nutritional importance. Despite having a significant agronomic role, little is known about the genetic and phenotypic diversity of cashew populations in Brazil. Thus, we aimed to characterize and estimate the diversity among cashew genotypes based on agro-morphological and physicochemical traits, with an objective of selection of varieties for breeding programmes. Forty-three cashew trees were evaluated based on 13 morphological traits and three physicochemical traits. A wide range of variations was recorded for the phenotypic characteristics, including total weight, fruit weight, pseudofruit length, kernel weight and total acidity, suggesting the existence of considerable variations for potential use in breeding programmes. Principal component analysis explained 79.74% of the total variation in the first two principal axes. The dendrogram based on the UPGMA method classified the 43 genotypes into six groups. Groups IV and VI were the most dissimilar, with emphasis on the genotypes 28 and 43, which were observed to be most divergent based on the Euclidean distance matrix (3.054). This makes it possible to select genotypes for hybridization with F1 generation gains. Based on cluster analysis and comparison of means among the six groups, promising genotypes were identified with superior traits, such as fruit weight, pseudofruit length, kernel weight and total acidity. This suggests the importance of phenotypic characterization for cashew breeding programmes. In addition, the observed vast diversity is an important genetic basis for improving cashew yield in northeastern Brazil.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"117 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76373340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-08DOI: 10.1017/s1479262123000126
Navneeti Chamoli, D. Prabha, Y. Negi, J. Chauhan
Angular leaf spot (ALS) caused by Pseudocercospora griseola is a major disease of french bean (Phaseolus vulgaris L.) worldwide. A good diversity of French bean is present in the Garhwal Himalayas of Uttarakhand, India, which is unexplored. The purpose of this study was to identify ALS-resistant accessions among local landraces of French bean in this region. One hundred seventy-six local accessions were collected from different villages of Garhwal, Uttarakhand. All the accessions were screened by four SCAR primers SN02 (Phg-2), SAA19, SM02, SBA16 (Phg-3), one STS primer TGA1.1 (Phg-1) and one SSR primer Pv-at006 (Phg-5). All the accessions were also screened for ALS resistance under field condition in the years 2019 and 2020. The disease-resistant score was recorded on 1–9 scale. After field screening, 48 accessions (19 resistant, 24 moderately resistant and five susceptible) were selected for in-vitro screening under screen house condition. These 46 accessions were artificially inoculated by two different isolates of P. griseola P5 and P9, which are the most virulent pathotype characterized by microbiology lab, College of Forestry, Tehri, Uttarakhand. After in-vitro screening, seven accessions (GFB-25, GFB-26, GFB-30, GFB-32, GFB-93, GFB-97 and GFB-136) were found resistant to both the isolates P5 and P9. The P. griseola-resistant accessions may further be used in future breeding programmes to develop new and more resistant varieties of French bean against ALS.
{"title":"Evaluation of French bean germplasm from Garhwal Himalayas for resistance to angular leaf spot","authors":"Navneeti Chamoli, D. Prabha, Y. Negi, J. Chauhan","doi":"10.1017/s1479262123000126","DOIUrl":"https://doi.org/10.1017/s1479262123000126","url":null,"abstract":"\u0000 Angular leaf spot (ALS) caused by Pseudocercospora griseola is a major disease of french bean (Phaseolus vulgaris L.) worldwide. A good diversity of French bean is present in the Garhwal Himalayas of Uttarakhand, India, which is unexplored. The purpose of this study was to identify ALS-resistant accessions among local landraces of French bean in this region. One hundred seventy-six local accessions were collected from different villages of Garhwal, Uttarakhand. All the accessions were screened by four SCAR primers SN02 (Phg-2), SAA19, SM02, SBA16 (Phg-3), one STS primer TGA1.1 (Phg-1) and one SSR primer Pv-at006 (Phg-5). All the accessions were also screened for ALS resistance under field condition in the years 2019 and 2020. The disease-resistant score was recorded on 1–9 scale. After field screening, 48 accessions (19 resistant, 24 moderately resistant and five susceptible) were selected for in-vitro screening under screen house condition. These 46 accessions were artificially inoculated by two different isolates of P. griseola P5 and P9, which are the most virulent pathotype characterized by microbiology lab, College of Forestry, Tehri, Uttarakhand. After in-vitro screening, seven accessions (GFB-25, GFB-26, GFB-30, GFB-32, GFB-93, GFB-97 and GFB-136) were found resistant to both the isolates P5 and P9. The P. griseola-resistant accessions may further be used in future breeding programmes to develop new and more resistant varieties of French bean against ALS.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"5 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76408899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-08DOI: 10.1017/s1479262123000114
Mozafar Sadeghikian, Abdollah Najaphy, D. Kahrizi, Hossein Rostami Amadvandi
Camelina (Camelina sativa (L.) Crantz), an oilseed crop, belongs to the Brassicaceae family. Two unique features of camelina in comparison with the main oil crops are an adaptation to different environments and also its unique oil composition. The development of doubled haploid plants is one of the essential methods for crop improvement. The study of genetic diversity is an important step in planning crop breeding programmes. This research was conducted to evaluate the genetic variation of 81 camelina doubled haploid lines obtained from 15 crosses by inter simple sequence repeat (ISSR) markers. The total number of amplified bands was 243, of which 239 bands (98.3%) showed polymorphism. The percentage of polymorphic bands varied between 93.75 and 100. The size of the bands ranged from 50 to 1700 base pairs. The informative ISSRs were identified by estimating marker features: polymorphism information content, effective multiplex ratio, marker index and resolving power. Three markers had higher resolving power values (9.88, 8.5 and 7.46) and were the most informative markers to identify the lines. Cluster analysis based on the complete algorithm divided the lines into five groups, indicating relatively clear configuration from the geographic distribution patterns of the parents of the doubled haploid lines. Principal coordinate analysis classified the 81 camelina doubled haploid lines into six groups. The ISSR markers detected high polymorphism to reveal the genetic variation of camelina lines. The findings of this research, along with the characterization of biochemical traits of the lines, can improve breeding programmes achieve high-yielding camelina varieties with higher and better oil content.
{"title":"Assessment of molecular diversity in doubled haploid lines of camelina (Camelina sativa (L.) Crantz), as a new emerging oil crop","authors":"Mozafar Sadeghikian, Abdollah Najaphy, D. Kahrizi, Hossein Rostami Amadvandi","doi":"10.1017/s1479262123000114","DOIUrl":"https://doi.org/10.1017/s1479262123000114","url":null,"abstract":"\u0000 Camelina (Camelina sativa (L.) Crantz), an oilseed crop, belongs to the Brassicaceae family. Two unique features of camelina in comparison with the main oil crops are an adaptation to different environments and also its unique oil composition. The development of doubled haploid plants is one of the essential methods for crop improvement. The study of genetic diversity is an important step in planning crop breeding programmes. This research was conducted to evaluate the genetic variation of 81 camelina doubled haploid lines obtained from 15 crosses by inter simple sequence repeat (ISSR) markers. The total number of amplified bands was 243, of which 239 bands (98.3%) showed polymorphism. The percentage of polymorphic bands varied between 93.75 and 100. The size of the bands ranged from 50 to 1700 base pairs. The informative ISSRs were identified by estimating marker features: polymorphism information content, effective multiplex ratio, marker index and resolving power. Three markers had higher resolving power values (9.88, 8.5 and 7.46) and were the most informative markers to identify the lines. Cluster analysis based on the complete algorithm divided the lines into five groups, indicating relatively clear configuration from the geographic distribution patterns of the parents of the doubled haploid lines. Principal coordinate analysis classified the 81 camelina doubled haploid lines into six groups. The ISSR markers detected high polymorphism to reveal the genetic variation of camelina lines. The findings of this research, along with the characterization of biochemical traits of the lines, can improve breeding programmes achieve high-yielding camelina varieties with higher and better oil content.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"12 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84784775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-07DOI: 10.1017/s1479262123000059
Pocovi Mariana, Maximiliano Sosa, R. Delgado, Verónica Castillo, Graciela Collavino, J. Carreras
In order to enhance genetic potential of chickpea materials from the National University of Córdoba Breeding Programme and Germplasm collection (Argentina), a study for a comprehensive understanding of the amount and pattern of genetic variation within and between genotypes was carried out by applying a multivariate analysis form single simple repeats (SSR) and morphological data. Molecular data were also used to determine the discriminating power for genotype identification, and to find the optimal primer combination to ensure unambiguous identification. With the analysis of 15 SSR markers on 53 genotypes, a total of 58 alleles were detected with individual values ranging from one to nine alleles per locus. High values of discriminating power (Dj ⩾ 0.7, PIC ⩾ 0.7), and low values of confusion probability (Cj ⩽ 0.23) were obtained for at least four evaluated markers. The combination of TA113 + TA114 + H1B09 + TA106 primers was effective for discriminating the 53 chickpea genotypes with a cumulative confusion probability value (Ck) of 9.60 × 10−4. Except for some exceptions, individual chickpea genotypes within a cluster in the consensus tree were definitely more closely related with each other by the origin or pedigree. The results confirmed that both multivariate data analysis methods, ordination and clustering, were complementary. In most genotypes, discriminant principal component analysis classification was consistent with the original clusters defined by molecular data. Differences in results from molecular and morphological data indicate that they provide complementary and relevant information for establishing genetic relationships among chickpea materials and a better description and interpretation of the available variability in the germplasm collection.
{"title":"Multivariate analysis from SSR and morphological data in chickpea (Cicer arietinum L.) for breeding purposes","authors":"Pocovi Mariana, Maximiliano Sosa, R. Delgado, Verónica Castillo, Graciela Collavino, J. Carreras","doi":"10.1017/s1479262123000059","DOIUrl":"https://doi.org/10.1017/s1479262123000059","url":null,"abstract":"\u0000 In order to enhance genetic potential of chickpea materials from the National University of Córdoba Breeding Programme and Germplasm collection (Argentina), a study for a comprehensive understanding of the amount and pattern of genetic variation within and between genotypes was carried out by applying a multivariate analysis form single simple repeats (SSR) and morphological data. Molecular data were also used to determine the discriminating power for genotype identification, and to find the optimal primer combination to ensure unambiguous identification. With the analysis of 15 SSR markers on 53 genotypes, a total of 58 alleles were detected with individual values ranging from one to nine alleles per locus. High values of discriminating power (Dj ⩾ 0.7, PIC ⩾ 0.7), and low values of confusion probability (Cj ⩽ 0.23) were obtained for at least four evaluated markers. The combination of TA113 + TA114 + H1B09 + TA106 primers was effective for discriminating the 53 chickpea genotypes with a cumulative confusion probability value (Ck) of 9.60 × 10−4. Except for some exceptions, individual chickpea genotypes within a cluster in the consensus tree were definitely more closely related with each other by the origin or pedigree. The results confirmed that both multivariate data analysis methods, ordination and clustering, were complementary. In most genotypes, discriminant principal component analysis classification was consistent with the original clusters defined by molecular data. Differences in results from molecular and morphological data indicate that they provide complementary and relevant information for establishing genetic relationships among chickpea materials and a better description and interpretation of the available variability in the germplasm collection.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"33 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82283570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.
{"title":"Development of a set of InDel markers for characterizing three japonica rice (Oryza sativa L.) varieties","authors":"Hongmei Wang, Yue Zhu, Chujian Xiao, Jian-Guo Yuan, Yaoguang Liu, Qunyu Zhang","doi":"10.1017/s1479262123000096","DOIUrl":"https://doi.org/10.1017/s1479262123000096","url":null,"abstract":"\u0000 The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"126 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88118134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-06DOI: 10.1017/s1479262123000060
Ana Cruz Morillo-Coronado, E. H. Manjarrés-Hernández, María Camila Pedreros-Benavides
Chenopodium quinoa W. is a species of South America with an exceptional nutritional content and wide agroclimatological adaptation. It has great genetic and phenotypic variability, however in Colombia there are few genetic improvement programmes that take advantage of its great genetic and productive potential. In Cundinamarca there are some adapted genotypes which have been selected by farmers. We evaluated 36 genotypes of Blanca de Jericó, Blanca Subachoque, Aurora, Púrpura and Tunkahuan from Cundinamarca, using eight ISSR markers. The analysis by the coefficient of Nei-Li at the level of similarity of 0.40 divided the population into three groups according their background genetic and the colour of oxalates. The percentage of polymorphic loci was higher than 90%. The average value of heterozygosity was 0.32, which is low given the selection processes that the evaluated germplasm has undergone. We found moderate genetic differentiation (Fst = 0.23). The analysis of molecular variance (AMOVA) showed higher variation (77%) groups than among groups (23%). The results revealed intra-population diversity, which suggests that farmers within their farms should undergo a more rigorous seed selection process. Our results demonstrate that ISSR markers are useful and powerful to assess the genetic relationships, polymorphism and genetic diversity of quinoa cultivars. The genetic characterization results reported in the present study will be promising for guiding the breeding of quinoa seed quality in Colombia.
藜麦(Chenopodium quinoa W.)是南美洲的一种，具有特殊的营养成分和广泛的农业气候适应性。它具有很大的遗传和表型变异性，但在哥伦比亚，利用其巨大的遗传和生产潜力的遗传改良方案很少。在Cundinamarca，农民选择了一些适应的基因型。利用8个ISSR标记，对来自Cundinamarca的Blanca de Jericó、Blanca Subachoque、Aurora、Púrpura和Tunkahuan的36个基因型进行了评价。在相似水平为0.40的Nei-Li系数分析中，根据草酸盐的背景遗传和颜色将群体分为3个群体。多态性位点的比例大于90%。杂合度平均值为0.32，考虑到被评价种质所经历的选择过程，这是一个较低的杂合度。我们发现中度遗传分化(Fst = 0.23)。分子方差(AMOVA)分析显示，组间变异率(23%)高于组间变异率(77%)。结果揭示了种群内的多样性，这表明农民在他们的农场内应该经历一个更严格的种子选择过程。研究结果表明，ISSR标记对藜麦品种的亲缘关系、多态性和遗传多样性的评价是有效的。本研究报告的遗传鉴定结果对指导哥伦比亚藜麦种子品质育种具有重要意义。
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Pub Date : 2023-03-01DOI: 10.1017/s1479262123000011
Y. A. Nanja Reddy
Screening of germplasm for specific traits is a continuous pre-breeding process in deriving the drought-tolerant donors required for crop improvement. The study evaluated 17 medium-late duration finger millet genotypes under drought stress (DS) for 28 days during the reproductive stage to identify the traits and genotypes for drought tolerance using different statistical analysis. The photosynthetic rate (by 26.3%), stomatal conductance (by 26.4%), transpiration rate (by 24.8%) and grain yield (by 13.2%) were decreased and found sensitive to DS, but the leaf temperature was increased (4.7%). From the path analysis and multiple linear regression analysis, the mean ear weight and productive tillers were found to contribute to the grain yield significantly under well-watered conditions. While under DS conditions, the mean ear weight, productive tillers and threshing percentage equally contributed to grain yield. Based on the ranking of traits significantly contributing to grain yield, the genotype GE-4683 with a higher mean ear weight (10.65 g) was found superior to the popular variety, GPU-28. The Multiple linear regression equation predicts the possibility to increase the yield of GPU-28 under DS from the existing 360.0 to 459.5 g per square metre (by 29.1%) by the incorporation of three productive tillers instead of the existing two tillers per plant in the MLR equation. An additional 1.0 g of mean ear weight will be able to predict an increased grain yield from 360.0 to 392.0 gm−2, equivalent to 3.60 to 3.92 t/ha (by 9.4%).
{"title":"Identification of yield contributing traits and genotypes to drought tolerance in finger millet (Eleusine coracana L. Gaertn.)","authors":"Y. A. Nanja Reddy","doi":"10.1017/s1479262123000011","DOIUrl":"https://doi.org/10.1017/s1479262123000011","url":null,"abstract":"\u0000 Screening of germplasm for specific traits is a continuous pre-breeding process in deriving the drought-tolerant donors required for crop improvement. The study evaluated 17 medium-late duration finger millet genotypes under drought stress (DS) for 28 days during the reproductive stage to identify the traits and genotypes for drought tolerance using different statistical analysis. The photosynthetic rate (by 26.3%), stomatal conductance (by 26.4%), transpiration rate (by 24.8%) and grain yield (by 13.2%) were decreased and found sensitive to DS, but the leaf temperature was increased (4.7%). From the path analysis and multiple linear regression analysis, the mean ear weight and productive tillers were found to contribute to the grain yield significantly under well-watered conditions. While under DS conditions, the mean ear weight, productive tillers and threshing percentage equally contributed to grain yield. Based on the ranking of traits significantly contributing to grain yield, the genotype GE-4683 with a higher mean ear weight (10.65 g) was found superior to the popular variety, GPU-28. The Multiple linear regression equation predicts the possibility to increase the yield of GPU-28 under DS from the existing 360.0 to 459.5 g per square metre (by 29.1%) by the incorporation of three productive tillers instead of the existing two tillers per plant in the MLR equation. An additional 1.0 g of mean ear weight will be able to predict an increased grain yield from 360.0 to 392.0 gm−2, equivalent to 3.60 to 3.92 t/ha (by 9.4%).","PeriodicalId":20252,"journal":{"name":"Plant Genetic Resources: Characterization and Utilization","volume":"71 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83880517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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