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Wang Y, Wang Z, Chen Y, Lan T, Wang X, Liu G, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Guo W, Peng H. Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding. Plant Commun 2024; 5:100883. [PMID: 38491771 PMCID: PMC11121738 DOI: 10.1016/j.xplc.2024.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/22/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Spelt (Triticum aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource. However, relatively little is known about the origins and maintenance of spelt populations. Here, using resequencing data from 416 worldwide wheat accessions, including representative spelt wheat, we demonstrate that European spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer, the putative maternal donor. Genomic introgression regions from domesticated emmer confer spelt's primitive morphological characters used for species taxonomy, such as tenacious glumes and later flowering. We propose a haplotype-based "spelt index" to identify spelt-type wheat varieties and to quantify utilization of the spelt gene pool in modern wheat cultivars. This study reveals the genetic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.
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Affiliation(s)
- Yongfa Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Tianyu Lan
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Institute for Plant Genetics, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Xiaobo Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Gang Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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Agdzhoyan A, Iskandarov N, Ponomarev G, Pylev V, Koshel S, Salaev V, Pocheshkhova E, Kagazezheva Z, Balanovska E. Origins of East Caucasus Gene Pool: Contributions of Autochthonous Bronze Age Populations and Migrations from West Asia Estimated from Y-Chromosome Data. Genes (Basel) 2023; 14:1780. [PMID: 37761920 PMCID: PMC10530682 DOI: 10.3390/genes14091780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The gene pool of the East Caucasus, encompassing modern-day Azerbaijan and Dagestan populations, was studied alongside adjacent populations using 83 Y-chromosome SNP markers. The analysis of genetic distances among 18 populations (N = 2216) representing Nakh-Dagestani, Altaic, and Indo-European language families revealed the presence of three components (Steppe, Iranian, and Dagestani) that emerged in different historical periods. The Steppe component occurs only in Karanogais, indicating a recent medieval migration of Turkic-speaking nomads from the Eurasian steppe. The Iranian component is observed in Azerbaijanis, Dagestani Tabasarans, and all Iranian-speaking peoples of the Caucasus. The Dagestani component predominates in Dagestani-speaking populations, except for Tabasarans, and in Turkic-speaking Kumyks. Each component is associated with distinct Y-chromosome haplogroup complexes: the Steppe includes C-M217, N-LLY22g, R1b-M73, and R1a-M198; the Iranian includes J2-M172(×M67, M12) and R1b-M269; the Dagestani includes J1-Y3495 lineages. We propose J1-Y3495 haplogroup's most common lineage originated in an autochthonous ancestral population in central Dagestan and splits up ~6 kya into J1-ZS3114 (Dargins, Laks, Lezgi-speaking populations) and J1-CTS1460 (Avar-Andi-Tsez linguistic group). Based on the archeological finds and DNA data, the analysis of J1-Y3495 phylogeography suggests the growth of the population in the territory of modern-day Dagestan that started in the Bronze Age, its further dispersal, and the microevolution of the diverged population.
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Affiliation(s)
| | - Nasib Iskandarov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Georgy Ponomarev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Vladimir Pylev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Biobank of Northern Eurasia, 115201 Moscow, Russia
| | - Sergey Koshel
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Cartography and Geoinformatics, Faculty of Geography, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vugar Salaev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Elvira Pocheshkhova
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Zhaneta Kagazezheva
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
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Wongloet W, Singchat W, Chaiyes A, Ali H, Piangporntip S, Ariyaraphong N, Budi T, Thienpreecha W, Wannakan W, Mungmee A, Jaisamut K, Thong T, Panthum T, Ahmad SF, Lisachov A, Suksavate W, Muangmai N, Chuenka R, Nunome M, Chamchumroon W, Han K, Nuangmek A, Matsuda Y, Duengkae P, Srikulnath K. Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken. Animals (Basel) 2023; 13:1949. [PMID: 37370459 PMCID: PMC10295432 DOI: 10.3390/ani13121949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.
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Affiliation(s)
- Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand;
| | - Hina Ali
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Surachai Piangporntip
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- School of Integrated Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Bureau of Conservation and Research, Zoological Park Organization of Thailand, Bangkok 10300, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Worawit Thienpreecha
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Wannapa Wannakan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Autchariyapron Mungmee
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Kittipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Warong Suksavate
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | | | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Ridai-cho 1-1, Kita-ku, Okayama 700-0005, Japan;
| | - Wiyada Chamchumroon
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand;
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Aniroot Nuangmek
- Mae Hong Son Provincial Livestock Office, Department of Livestock Development, Ministry of Agriculture and Cooperatives, Mae Hong Son 58000, Thailand;
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- School of Integrated Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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Kharkov VN, Kolesnikov NA, Valikhova LV, Zarubin AA, Svarovskaya MG, Marusin AV, Khitrinskaya IY, Stepanov VA. Relationship of the gene pool of the Khants with the peoples of Western Siberia, Cis-Urals and the Altai-Sayan Region according to the data on the polymorphism of autosomic locus and the Y-chromosome. Vavilovskii Zhurnal Genet Selektsii 2023; 27:46-54. [PMID: 36923476 PMCID: PMC10009483 DOI: 10.18699/vjgb-23-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 03/18/2023] Open
Abstract
Khanty are indigenous Siberian people living on the territory of Western Siberia, mainly on the territory of the Khanty-Mansiysk and Yamalo-Nenets Autonomous Okrugs. The present study is aimed at a comprehensive analysis of the structure of the Khanty gene pool and their comparison with other populations of the indigenous population of Southern and Western Siberia. To address the issues of genetic proximity of the Khanty with other indigenous peoples, we performed genotyping of a wide genomic set of autosomal markers using high-density biochips, as well as an expanded set of SNP and STR markers of the Y-chromosome in various ethnic groups: Khakas, Tuvans, Southern Altaians, Siberian Tatars, Chulyms (Turkic language family) and Kets (Yeniseian language family). The structure of the gene pool of the Khanty and other West Siberian and South Siberian populations was studied using a genome-wide panel of autosomal single nucleotide polymorphic markers and Y-chromosome markers. The results of the analysis of autosomal SNPs frequencies by various methods, the similarities in the composition of the Y-chromosome haplogroups and YSTR haplotypes indicate that the Khanty gene pool is quite specific. When analyzing autosomal SNPs, the Ugrian genetic component completely dominates in both samples (up to 99-100 %). The samples of the Khanty showed the maximum match in IBD blocks with each other, with a sample of the Kets, Chulyms, Tuvans, Tomsk Tatars, Khakas, Kachins, and Southern Altaians. The degree of coincidence of IBD blocks between the Khanty, Kets, and Tomsk Tatars is consistent with the results of the distribution of allele frequencies and common genetic components in these populations. According to the composition of the Y-chromosome haplogroups, the two samples of the Khanty differ significantly from each other. A detailed phylogenetic analysis of various Y-chromosome haplogroups made it possible to describe and clarify the differences in the phylogeny and structure of individual ethnospecific sublines, to determine their relationship, traces of population expansion in the Khanty gene pool. Variants of different haplogroups of the Y-chromosome in the Khanty, Khakas and Tuvans go back to their common ancestral lines. The results of a comparative analysis of male samples indicate a close genetic relationship between the Khanty and Nenets, Komi, Udmurts and Kets. The specificity of haplotypes, the discovery of various terminal SNPs confirms that the Khanty did not come into contact with other ethnic groups for a long time, except for the Nenets, which included many Khanty clans.
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Affiliation(s)
- V N Kharkov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N A Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - L V Valikhova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - M G Svarovskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A V Marusin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I Yu Khitrinskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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Stepanov VA, Kolesnikov NA, Valikhova LV, Zarubin AA, Khitrinskaya IY, Kharkov VN. Structure and origin of Tuvan gene pool according to autosome SNP and Y-chromosome haplogroups. Vavilovskii Zhurnal Genet Selektsii 2023; 27:36-45. [PMID: 36923480 PMCID: PMC10009474 DOI: 10.18699/vjgb-23-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 03/11/2023] Open
Abstract
Tuvans are one of the most compactly living peoples of Southern Siberia, settled mainly in the territory of Tuva. The gene pool of the Tuvans is quite isolated, due to endogamy and a very low frequency of interethnic marriages. The structure of the gene pool of the Tuvans and other Siberian populations was studied using a genome-wide panel of autosomal single nucleotide polymorphic markers and Y-chromosome markers. The results of the analysis of the frequencies of autosomal SNPs by various methods, the similarities in the composition of the Y-chromosome haplogroups and YSTR haplotypes show that the gene pool of the Tuvans is very heterogeneous in terms of the composition of genetic components. It includes the ancient autochthonous Yeniseian component, which dominates among the Chulym Turks and Kets, the East Siberian component, which prevails among the Yakuts and Evenks, and the Far Eastern component, the frequency of which is maximum among the Nivkhs and Udeges. Analysis of the composition of IBD-blocks on autosomes shows the maximum genetic relationship of the Tuvans with the Southern Altaians, Khakas and Shors, who were formed during the settlement of the Turkic groups of populations on the territory of the Altai-Sayan region. A very diverse composition of the Tuvan gene pool is shown for various sublines of Y-chromosomal haplogroups, most of which show strong ethnic specificity. Phylogenetic analysis of individual Y-chromosome haplogroups demonstrates the maximum proximity of the gene pool of the Tuvans with the Altaians, Khakas and Shors. Differences in frequencies of Y-chromosome haplogroups between the Todzhans and Tuvans and a change in the frequencies of haplogroups from south to north associated with the East Asian component were found. The majority of the most frequent Y-chromosome haplogroups in the Tuvans demonstrate the founder effect, the formation age of which is fully consistent with the data on their ethnogenesis.
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Affiliation(s)
- V A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N A Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - L V Valikhova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I Yu Khitrinskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V N Kharkov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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Wei Y, He S, Wang J, Fan P, He Y, Hu K, Chen Y, Zhou G, Zhong D, Zheng X. Genome-wide SNPs reveal novel patterns of spatial genetic structure in Aedes albopictus (Diptera Culicidae) population in China. Front Public Health 2022; 10:1028026. [PMID: 36438226 PMCID: PMC9685676 DOI: 10.3389/fpubh.2022.1028026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Since the second half of the 20th century, Aedes albopictus, a vector for more than 20 arboviruses, has spread worldwide. Aedes albopictus is the main vector of infectious diseases transmitted by Aedes mosquitoes in China, and it has caused concerns regarding public health. A comprehensive understanding of the spatial genetic structure of this vector species at a genomic level is essential for effective vector control and the prevention of vector-borne diseases. Methods During 2016-2018, adult female Ae. albopictus mosquitoes were collected from eight different geographical locations across China. Restriction site-associated DNA sequencing (RAD-seq) was used for high-throughput identification of single nucleotide polymorphisms (SNPs) and genotyping of the Ae. albopictus population. The spatial genetic structure was analyzed and compared to those exhibited by mitochondrial cytochrome c oxidase subunit 1 (cox1) and microsatellites in the Ae. albopictus population. Results A total of 9,103 genome-wide SNP loci in 101 specimens and 32 haplotypes of cox1 in 231 specimens were identified in the samples from eight locations in China. Principal component analysis revealed that samples from Lingshui and Zhanjiang were more genetically different than those from the other locations. The SNPs provided a better resolution and stronger signals for novel spatial population genetic structures than those from the cox1 data and a set of previously genotyped microsatellites. The fixation indexes from the SNP dataset showed shallow but significant genetic differentiation in the population. The Mantel test indicated a positive correlation between genetic distance and geographical distance. However, the asymmetric gene flow was detected among the populations, and it was higher from south to north and west to east than in the opposite directions. Conclusions The genome-wide SNPs revealed seven gene pools and fine spatial genetic structure of the Ae. albopictus population in China. The RAD-seq approach has great potential to increase our understanding of the spatial dynamics of population spread and establishment, which will help us to design new strategies for controlling vectors and mosquito-borne diseases.
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Affiliation(s)
- Yong Wei
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China,Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Song He
- Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Jiatian Wang
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Peiyang Fan
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yulan He
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ke Hu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yulan Chen
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Guofa Zhou
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Xueli Zheng
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China,*Correspondence: Xueli Zheng
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Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. Front Plant Sci 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Hanifei M, Gholizadeh A, Khodadadi M, Mehravi S, Hanifeh M, Edwards D, Batley J. Dissection of Genetic Effects, Heterosis, and Inbreeding Depression for Phytochemical Traits in Coriander. Plants (Basel) 2022; 11:plants11212959. [PMID: 36365411 PMCID: PMC9654661 DOI: 10.3390/plants11212959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/24/2022] [Accepted: 10/29/2022] [Indexed: 05/09/2023]
Abstract
Increasing seed yield, fatty acids, and essential oil content are the main objectives in breeding coriander. However, in order to achieve this, there is a need to understand the nature of gene action and quantify the heterosis and inbreeding depression. Towards this, six genetically diverse parents, their 15 F1 one-way hybrids, and 15 F2 populations were evaluated under different water treatments. The genetic effects of general (GCA) and specific combining ability (SCA) and their interactions with water treatment were significant for five traits. Water deficit stress decreased all traits in both F1 and F2 generations except for the essential oil content, which was significantly increased due to water deficit stress. Under water deficit stress, a non-additive gene action was predominant in the F1 generation, while an additive gene action was predominant in the F2 generation for all the traits except seed yield under severe water deficit stress. There was a positive high heterosis for the traits examined in some hybrids. Furthermore, in the F2 generation, even after inbreeding depression, some promising populations displayed appropriate mean performance. The results show that the parents used for crossing had a rich, diverse gene pool for the traits studied. Therefore, selection between the individuals of relevant F2 populations could be used to develop high yielding hybrids or superior lines.
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Affiliation(s)
- Mehrdad Hanifei
- Department of Plant Genetics and Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran C.P. 14115-336, Iran
| | - Amir Gholizadeh
- Crop and Horticultural Science Research Department, Golestan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Gorgan C.P. 19395-1113, Iran
| | - Mostafa Khodadadi
- Seed and Plant Improvement Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj C.P. 33151-31359, Iran
| | - Shaghayegh Mehravi
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Mehnosh Hanifeh
- Department of Plant Production and Genetics, Faculty of Agriculture, Malayer University, Malayer C.P. 65719-95863, Iran
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
- Correspondence: ; Tel.: +61-8-64885929
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Dementieva NV, Shcherbakov YS, Tyshchenko VI, Terletsky VP, Vakhrameev AB, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbah NR, Griffin DK, Romanov MN. Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds. Genes (Basel) 2022; 13:genes13101876. [PMID: 36292761 PMCID: PMC9601448 DOI: 10.3390/genes13101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence: (N.V.D.); (M.N.R.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Anatoly B. Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anna E. Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Grigoriy K. Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia R. Reinbah
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence: (N.V.D.); (M.N.R.)
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10
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Suprayogi TW, Susilowati S, Hernawati T, Hafidha FG, Wening CA, Purnawan AB. Improved quality of Kambing Kacang sexing frozen semen with the addition of green tea extract. J Adv Vet Anim Res 2022; 9:412-418. [PMID: 36382036 PMCID: PMC9597917 DOI: 10.5455/javar.2022.i609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
Objective The objective of this study was to determine the effect of adding various doses of green tea extract to the semen of Kacang goats during the sexing process on motility, viability, membrane integrity, malondialdehide (MDA), and deoxyribonucleic acid (DNA) fragmentation. Materials and Methods It started with the containment of the semen of the Kacang goat, followed by macroscopic and microscopic examinations. If the semen was considered viable, a diluter that had been added with various doses of green tea extract would be added to the semen. After that, sexing was carried out using the percoll gradient density medium. Next, the sexed semen was cryopreserved in liquid nitrogen. Then, an examination of motility, viability, membrane integrity, MDA, and DNA fragmentation was conducted. Result There was a significant difference between the control and treatment (p ≤ 0.05). The highest result was obtained in the treatment of adding 0.05 mg of green tea extract/100 ml of Andromed®. Conclusion The addition of green tea extract can improve the quality of the sexed semen of the Kacang goat after it has been cryopreserved.
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Affiliation(s)
- Tri Wahyu Suprayogi
- Department of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Suherni Susilowati
- Department of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Tatik Hernawati
- Department of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Farah Ghifara Hafidha
- Department of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Citra Ayu Wening
- Department of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
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Choudhary AK, Jain SK, Dubey AK, Kumar J, Sharma M, Gupta KC, Sharma LD, Prakash V, Kumar S. Conventional and molecular breeding for disease resistance in chickpea: status and strategies. Biotechnol Genet Eng Rev 2022:1-32. [PMID: 35959728 DOI: 10.1080/02648725.2022.2110641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 12/21/2021] [Indexed: 11/02/2022]
Abstract
Chickpea (Cicer arietinum L.) is an important grain legume at the global level. Among different biotic stresses, diseases are the most important factor limiting its production, causing yield losses up to 100% in severe condition. The major diseases that adversely affect yield of chickpea include Fusarium wilt, Ascochyta blight and Botrytis gray mold. However, dry root rot, collar rot, Sclerotinia stem rot, rust, stunt disease and phyllody have been noted as emerging biotic threats to chickpea production in many production regions. Identification and incorporation of different morphological and biochemical traits are required through breeding to enhance genetic gain for disease resistance. In recent years, remarkable progress has been made in the development of trait-specific breeding lines, genetic and genomic resources in chickpea. Advances in genomics technologies have opened up new avenues to introgress genes from secondary and tertiary gene pools for improving disease resistance in chickpea. In this review, we have discussed important diseases, constraints and improvement strategies for enhancing disease resistance in chickpea.
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Affiliation(s)
- Arbind K Choudhary
- Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Shailesh Kumar Jain
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Abhishek Kumar Dubey
- Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Jitendra Kumar
- Division of Crop Improvement, Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Mamta Sharma
- Crop Protection and Seed Health, International Crops Research Institute for the Semi-Arid-Tropics (ICRISAT), Patancheru, Telangana, India
| | - Kailash Chand Gupta
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Leela Dhar Sharma
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Ved Prakash
- Department of Genetics and Plant Breeding, Rajasthan Agricultural Research Institute, Durgapura, Jaipur, Rajasthan, India
| | - Saurabh Kumar
- Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, Bihar, India
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12
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Mirheidari F, Khadivi A, Saeidifar A, Moradi Y. Selection of superior genotypes of Indian jujube ( Ziziphus mauritiana Lamk.) as revealed by fruit-related traits. Food Sci Nutr 2022; 10:903-913. [PMID: 35311171 PMCID: PMC8907730 DOI: 10.1002/fsn3.2721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022] Open
Abstract
The nutritional and medicinal benefits of Ziziphus mauritiana Lamk. have led to its attention. Here, morphological and pomological diversity of this species was investigated. Most of the characters recorded showed considerable differences among the genotypes studied. The range of ripening data was from mid-February to mid-March. Fruit weight ranged between 15.68 and 33.62 g with an average of 24.17. Strong diversity was observed among the genotypes in terms of fruit skin ground color, ranging from light green to orange. There were significant correlations between some characters especially between the traits related to fruit size. Principal component analysis (PCA) classified the traits into 12 main components, justifying 75.07% of the total variance. The studied genotypes were grouped into two main clusters, indicating strong diversity among them. The present information might be used to choose the genotypes with the desired traits. Twenty-one genotypes were promising because of high values of fruit weight, fruit taste, fruit skin color, and fruit quality, and thus, they can be recommended for direct cultivation and also to be used in breeding programs. The genotypes with superior traits can be further used for improvement through selection and hybridization to get desired traits.
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Affiliation(s)
- Farhad Mirheidari
- Department of Horticultural Sciences Faculty of Agriculture and Natural Resources Arak University Arak Iran
| | - Ali Khadivi
- Department of Horticultural Sciences Faculty of Agriculture and Natural Resources Arak University Arak Iran
| | | | - Younes Moradi
- Department of Horticultural Sciences Faculty of Agriculture and Natural Resources Arak University Arak Iran
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Perrino EV, Wagensommer RP. Crop Wild Relatives (CWRs) Threatened and Endemic to Italy: Urgent Actions for Protection and Use. Biology (Basel) 2022; 11:biology11020193. [PMID: 35205060 PMCID: PMC8869772 DOI: 10.3390/biology11020193] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022]
Abstract
An updated overview of the 29 threatened crop wild relatives (CWRs) endemic to Italy is presented, namely: Arrhenatherum elatius subsp. nebrodense, Barbarea rupicola, Brassica baldensis, Brassica glabrescens, Brassica macrocarpa, Brassica rupestris subsp. hispida, Brassica rupestris subsp. rupestris, Brassica tardarae, Brassicatrichocarpa, Brassica tyrrhena, Brassica villosa subsp. bivonana, Brassica villosa subsp. brevisiliqua, Brassica villosa subsp. drepanensis, Brassica villosa subsp. tineoi, Brassica villosa subsp. villosa, Daucus broteroi, Daucus carota subsp. rupestris, Daucus nebrodensis, Diplotaxis scaposa, Festuca centroapenninica, Lathyrus apenninus, Lathyrus odoratus, Malus crescimannoi, Phalaris arundinacea subsp. rotgesii, Vicia brulloi, Vicia consentina, Vicia giacominiana, Vicia ochroleuca subsp. ochroleuca, Vicia tenuifolia subsp. elegans. Data concerning geographical distribution, ecology (including plant communities and habitats of the Directive 92/43/EEC), genetics (chromosome number, breeding system, and/or the existence of gene pools), threat status at the national and international level (Red Lists), key plant properties, and in situ and ex situ conservation were analyzed and shown. At present, most of the listed endemic CWRs, 23 out of 29, have no gene pool at all, so they are CWRs only according to the taxon group and not according to the gene pool concept. In addition, there is a serious lack of data on the ex situ conservation in gene banks, with 16 species identified as high priority (HP) while 22 taxa have high priority (A) for in situ conservation. With the aim of their protection, conservation, and valorization, specific and urgent actions are recommended.
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Affiliation(s)
- Enrico Vito Perrino
- CIHEAM, Mediterranean Agronomic Institute of Bari, Via Ceglie 9, 70010 Valenzano, Italy
- Correspondence: or
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Mostafaei Dehnavi M, Ebadi A, Peirovi A, Taylor G, Salami SA. THC and CBD Fingerprinting of an Elite Cannabis Collection from Iran: Quantifying Diversity to Underpin Future Cannabis Breeding. Plants (Basel) 2022; 11:plants11010129. [PMID: 35009133 PMCID: PMC8747537 DOI: 10.3390/plants11010129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 05/05/2023]
Abstract
Cannabis (Cannabis sativa L.) has a rich history of human use, and the therapeutic importance of compounds produced by this species is recognized by the medical community. The active constituents of cannabis, collectively called cannabinoids, encompass hundreds of distinct molecules, the most well-characterized of which are tetrahydrocannabinol (THC) and cannabidiol (CBD), which have been used for centuries as recreational drugs and medicinal agents. As a first step to establish a cannabis breeding program, we initiated this study to describe the HPLC-measured quantity of THC and CBD biochemistry profiles of 161 feral pistillate cannabis plants from 20 geographical regions of Iran. Our data showed that Iran can be considered a new region of high potential for distribution of cannabis landraces with diverse THC and CBD content, predominantly falling into three groups, as Type I = THC-predominant, Type II = approximately equal proportions of THC and CBD (both CBD and THC in a ratio close to the unity), and Type III = CBD-predominant. Correlation analysis among two target cannabinoids and environmental and geographical variables indicated that both THC and CBD contents were strongly influenced by several environmental-geographical factors, such that THC and CBD contents were positively correlated with mean, min and max annual temperature and negatively correlated with latitude, elevation, and humidity. Additionally, a negative correlation was observed between THC and CBD concentrations, suggesting that further studies to unravel these genotype × environment interactions (G × E interactions) are warranted. The results of this study provide important pre-breeding information on a collection of cannabis that will underpin future breeding programs.
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Affiliation(s)
- Mahboubeh Mostafaei Dehnavi
- Department of Horticultural Sciences, Faculty of Engineering and Agricultural Science, University of Tehran, Karaj 31587-77871, Iran; (M.M.D.); (A.E.)
| | - Ali Ebadi
- Department of Horticultural Sciences, Faculty of Engineering and Agricultural Science, University of Tehran, Karaj 31587-77871, Iran; (M.M.D.); (A.E.)
| | - Afshin Peirovi
- CIAN Diagnostics, 5330 Spectrum Drive, Suite I, Frederick, MD 21703, USA;
| | - Gail Taylor
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
- Correspondence: (G.T.); (S.A.S.); Tel.: +1-530-752-9165 (G.T.); +98-2632248721 (S.A.S.)
| | - Seyed Alireza Salami
- Department of Horticultural Sciences, Faculty of Engineering and Agricultural Science, University of Tehran, Karaj 31587-77871, Iran; (M.M.D.); (A.E.)
- Industrial and Medical Cannabis Research Institute (IMCRI), Tehran 14176-14411, Iran
- Correspondence: (G.T.); (S.A.S.); Tel.: +1-530-752-9165 (G.T.); +98-2632248721 (S.A.S.)
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15
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Wu Q, Wang Y, Liu LN, Shi K, Li CY. Comparative Genomics and Gene Pool Analysis Reveal the Decrease of Genome Diversity and Gene Number in Rice Blast Fungi by Stable Adaption with Rice. J Fungi (Basel) 2021; 8:jof8010005. [PMID: 35049945 PMCID: PMC8778285 DOI: 10.3390/jof8010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/12/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Magnaporthe oryzae caused huge losses in rice and wheat production worldwide. Comparing to long-term co-evolution history with rice, wheat-infecting isolates were new-emerging. To reveal the genetic differences between rice and wheat blast on global genomic scale, 109 whole-genome sequences of M. oryzae from rice, wheat, and other hosts were reanalyzed in this study. We found that the rice lineage had gone through stronger selective sweep and fewer conserved genes than those of Triticum and Lolium lineages, which indicated that rice blast fungi adapted to rice by gene loss and rapid evolution of specific loci. Furthermore, 228 genes associated with host adaptation of M. oryzae were found by presence/absence variation (PAV) analyses. The functional annotation of these genes found that the fine turning of genes gain/loss involved with transport and transcription factor, thiol metabolism, and nucleotide metabolism respectively are major mechanisms for rice adaption. This result implies that genetic base of specific host plant may lead to gene gain/loss variation of pathogens, so as to enhance their adaptability to host. Further characterization of these specific loci and their roles in adaption and evaluation of the fungi may eventually lead to understanding of interaction mechanism and develop new strategies of the disease management.
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Affiliation(s)
- Qi Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- College of Science, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
| | - Li-Na Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650201, China
| | - Kai Shi
- School of Foreign Language, Yunnan Agricultural University, Kunming 650201, China;
| | - Cheng-Yun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Correspondence:
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16
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Vishnyakova MA, Vlasova EV, Egorova GP. Genetic resources of narrow-leaved lupine (Lupinus angustifolius L.) and their role in its domestication and breeding. Vavilovskii Zhurnal Genet Selektsii 2021; 25:620-630. [PMID: 34782881 PMCID: PMC8558922 DOI: 10.18699/vj21.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/03/2022] Open
Abstract
Narrow-leaved lupine (Lupinus angustifolius L.) is a cultivated multipurpose species with a very short history of domestication. It is used as a green manure, and for feed and food. This crop shows good prospects for use in pharmacology and as a source of f ish feeds in aquaculture. However, its genetic potential for the development of productive and adaptable cultivars is far from being realized. For crop species, the genetic base of the cultivated gene pool has repeatedly been shown as being much narrower than that of the wild gene pool. Therefore, eff icient utilization of a species’ genetic resources is important for the crop’s further improvement. Analyzing the information on the germplasm collections preserved in national gene banks can help perceive the worldwide diversity of L. angustifolius genetic resources and understand how they are studied and used. In this context, the data on the narrow-leaved lupine collection held by VIR are presented: its size and composition, the breeding status of accessions, methods of studying and disclosing intraspecif ic differentiation, the classif ications used, and the comparison of this information with available data on other collections. It appeared that VIR’s collection of narrow-leaved lupine, ranking as the world’s second largest, differed signif icantly from others by the prevalence of advanced cultivars and breeding material in it, while wild accessions prevailed in most collections. The importance of the wild gene pool for the narrow-leaved lupine breeding in Australia, the world leader in lupine production, is highlighted. The need to get an insight into the species’ ecogeographic diversity in order to develop cultivars adaptable to certain cultivation conditions is shown. The data on the testing of VIR’s collection for main crop characters valuable for breeders are presented. Special attention is paid to the study of accessions with limited branching as a promising gene pool for cultivation in relatively northern regions of Russia. They demonstrate lower but more stable productivity, and suitability for cultivation in planting patterns, which has a number of agronomic advantages. Analyzing the work with narrow-leaved lupine genetic resources in different national gene banks over the world helps shape the prospects of further activities with VIR’s collection as the only source of promising material for domestic breeding.
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Affiliation(s)
- M A Vishnyakova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - E V Vlasova
- Federal Horticultural Research Center for Breeding, Agrotechnology and Nursery, Moscow, Russia
| | - G P Egorova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
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17
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Safdari L, Khadivi A. Identification of the promising oleaster ( Elaeagnus angustifolia L.) genotypes based on fruit quality-related characters. Food Sci Nutr 2021; 9:5712-5721. [PMID: 34646539 PMCID: PMC8498070 DOI: 10.1002/fsn3.2536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 11/08/2022] Open
Abstract
The fruits of oleaster (Elaeagnus angustifolia L.) are rich in nutritional value and contain protein, sugar, vitamins, and minerals. The present investigation was performed to evaluate the morphological variability of the naturally grown accessions of this species. There was considerable variation among the accessions based on all the traits measured. The range of fruit weight was from 0.32 to 3.04 g, with an average of 1.48. Fruit yield was significantly and positively correlated with tree growth vigor, canopy density, branching, branch density, and leaf density. Principal component analysis (PCA) indicated nine components of data accounted for 74.93% of the total variance. Ward cluster analysis using Euclidean distance classified the accessions into two main clusters and showed significant differences among the accessions studied. Among the area studied, 14 accessions showed the highest value of fruit quality-related characters, which are suitable for fresh consumption and health benefits. The results provided important information useful for selecting the preferred accessions for commercial cultivation and breeding programs.
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Affiliation(s)
- Leila Safdari
- Department of Horticultural SciencesFaculty of Agriculture and Natural ResourcesArak UniversityArakIran
| | - Ali Khadivi
- Department of Horticultural SciencesFaculty of Agriculture and Natural ResourcesArak UniversityArakIran
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18
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Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. Plant Biotechnol J 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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19
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Cliffe RN, Robinson CV, Whittaker BA, Kennedy SJ, Avey‐Arroyo JA, Consuegra S, Wilson RP. Genetic divergence and evidence of human-mediated translocation of two-fingered sloths (C holoepus hoffmanni) in Costa Rica. Evol Appl 2020; 13:2439-2448. [PMID: 33005232 PMCID: PMC7513709 DOI: 10.1111/eva.13036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/01/2022] Open
Abstract
Sloths are notoriously slow and consequently have limited dispersal ability, which makes them particularly vulnerable to the effects of habitat fragmentation and degradation. Sloths in Costa Rica are considered of conservation concern due to habitat loss, livestock production and increasing urbanization. Reintroductions from rescue centres are commonplace across the country, yet their genetic diversity and population structure are unknown, and there is currently little consideration of the genetic background prior to intervention or releases. We used microsatellite analysis to undertake the first exploratory investigation into sloth population genetics in Costa Rica. Using data from 98 two-fingered sloths (Choloepus hoffmanni) from four different geographic regions, we determined the presence of four potential genetic groups, three of them with minimal population structuring despite the limited dispersal ability and presence of physical barriers. Sloths from the North appear to represent a highly distinct population that we propose may require management as a discrete unit for conservation. We stress the need for additional analyses to better understand the genetic structure and diversity of North andWest regions and suggest that rescue facilities in Costa Rica should consider the genetic background of rehabilitated sloths when planning future reintroductions. Our results also highlight the threat posed by physical isolation due to widespread urbanization and agriculture expansion for a species with a weak dispersal ability.
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Affiliation(s)
- Rebecca N. Cliffe
- Biosciences, College of ScienceSwansea UniversityWalesUK
- The Sloth Sanctuary of Costa RicaLimonCosta Rica
- The Sloth Conservation FoundationHayfieldUK
| | - Chloe V. Robinson
- Biosciences, College of ScienceSwansea UniversityWalesUK
- Present address:
Department of Integrative Biology and Centre for Biodiversity GenomicsUniversity of Guelph50 Stone Road EGuelphONN1G 2W1Canada
| | - Benjamin A. Whittaker
- Biosciences, College of ScienceSwansea UniversityWalesUK
- The Sloth Sanctuary of Costa RicaLimonCosta Rica
- Present address:
Department of Integrative BiologyUniversity of Guelph50 Stone Road EGuelphONN1G 2W1Canada
| | | | | | | | - Rory P. Wilson
- Biosciences, College of ScienceSwansea UniversityWalesUK
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20
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Salazar A, Rousk K, Jónsdóttir IS, Bellenger J, Andrésson ÓS. Faster nitrogen cycling and more fungal and root biomass in cold ecosystems under experimental warming: a meta-analysis. Ecology 2020; 101:e02938. [PMID: 31750541 PMCID: PMC7027553 DOI: 10.1002/ecy.2938] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/01/2019] [Accepted: 10/18/2019] [Indexed: 11/13/2022]
Abstract
Warming can alter the biogeochemistry and ecology of soils. These alterations can be particularly large in high northern latitude ecosystems, which are experiencing the most intense warming globally. In this meta-analysis, we investigated global trends in how experimental warming is altering the biogeochemistry of the most common limiting nutrient for biological processes in cold ecosystems of high northern latitudes (>50°): nitrogen (N). For comparison, we also analyzed cold ecosystems at intermediate and high southern latitudes. In addition, we examined N-relevant genes and enzymes, and the abundance of belowground organisms. Together, our findings suggest that warming in cold ecosystems increases N mineralization rates and N2 O emissions and does not affect N fixation, at least not in a consistent way across biomes and conditions. Changes in belowground N fluxes caused by warming lead to an accumulation of N in the forms of dissolved organic and root N. These changes seem to be more closely linked to increases in enzyme activity that target relatively labile N sources, than to changes in the abundance of N-relevant genes (e.g., amoA and nosZ). Finally, our analysis suggests that warming in cold ecosystems leads to an increase in plant roots, fungi, and (likely in an indirect way) fungivores, and does not affect the abundance of archaea, bacteria, or bacterivores. In summary, our findings highlight global trends in the ways warming is altering the biogeochemistry and ecology of soils in cold ecosystems, and provide information that can be valuable for prediction of changes and for management of such ecosystems.
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Affiliation(s)
- Alejandro Salazar
- Faculty of Life and Environmental SciencesUniversity of IcelandSturlugata 7101ReykjavíkIceland
| | - Kathrin Rousk
- Department of BiologyTerrestrial Ecology SectionUniversity of CopenhagenUniversitetsparken 152100CopenhagenDenmark
- Center for Permafrost (CENPERM)University of CopenhagenØster Voldgade 101350CopenhagenDenmark
| | - Ingibjörg S. Jónsdóttir
- Faculty of Life and Environmental SciencesUniversity of IcelandSturlugata 7101ReykjavíkIceland
| | - Jean‐Philippe Bellenger
- Centre SeveDepartment of ChemistryFaculty of SciencesUniversite de SherbrookeJ1K2R1SherbrookeQuebecCanada
| | - Ólafur S. Andrésson
- Faculty of Life and Environmental SciencesUniversity of IcelandSturlugata 7101ReykjavíkIceland
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21
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Oladzad A, Porch T, Rosas JC, Moghaddam SM, Beaver J, Beebe SE, Burridge J, Jochua CN, Miguel MA, Miklas PN, Raatz B, White JW, Lynch J, McClean PE. Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments. G3 (Bethesda) 2019; 9:1881-1892. [PMID: 31167806 PMCID: PMC6553540 DOI: 10.1534/g3.119.400072] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/07/2019] [Indexed: 12/28/2022]
Abstract
The genetic improvement of economically important production traits of dry bean (Phaseolus vulgaris L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the P. vulgaris genome sequence. Moderately sized B ean A biotic S tress E valuation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs.
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Affiliation(s)
- Atena Oladzad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102
| | - Timothy Porch
- USDA-ARS, Tropical Agricultural Research Station Mayaguez Puerto Rico
| | - Juan Carlos Rosas
- Department of Agricultural Engineering, Zamorano University, Zamorano, Honduras
| | - Samira Mafi Moghaddam
- Plant Resilience Institute, Department of Plant Biology, Michigan State University, East Lansing, MI, 48824
| | - James Beaver
- Department of Agronomy and Soils, University of Puerto Rico, Mayaguez, Puerto Rico 00680
| | - Steve E Beebe
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Jimmy Burridge
- Department of Plant Science, Pennsylvania State University, State Collage, PA, 16801
| | | | | | - Phillip N Miklas
- USDA-ARS, Grain Legume Genetics Physiology Research, Prosser, WA
| | - Bodo Raatz
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Jeffery W White
- USDA-ARS, Plant Physiology and Genetics Research Maricopa, AZ
| | - Jonathan Lynch
- Department of Plant Science, Pennsylvania State University, State Collage, PA, 16801
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102
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22
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Park SC, Lee K, Kim YO, Won S, Chun J. Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size. Front Microbiol 2019; 10:834. [PMID: 31068915 PMCID: PMC6491781 DOI: 10.3389/fmicb.2019.00834] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified, because most studies have used a small number of genomes. Here, we constructed pan-genomes of seven species in order to elucidate variations in the genetic contents of >27,000 genomes belonging to Streptococcus pneumoniae, Staphylococcus aureus subsp. aureus, Salmonella enterica subsp. enterica, Escherichia coli and Shigella spp., Mycobacterium tuberculosis complex, Pseudomonas aeruginosa, and Acinetobacter baumannii. This work showed the pan-genomes of all seven species has open property. Additionally, systematic evaluation of the characteristics of their pan-genome revealed that phylogenetic distance provided valuable information for estimating the parameters for pan-genome size among several models including Heaps' law. Our results provide a better understanding of the species and a solution to minimize sampling biases associated with genome-sequencing preferences for pathogenic strains.
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Affiliation(s)
- Sang-Cheol Park
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Yeong Ouk Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Sungho Won
- Institute of Health and Environment, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.,Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.,Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
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Rivera A, Plans M, Sabaté J, Casañas F, Casals J, Rull A, Simó J. The Spanish Core Collection of Common Beans ( Phaseolus vulgaris L.): An Important Source of Variability for Breeding Chemical Composition. Front Plant Sci 2018; 9:1642. [PMID: 30483294 PMCID: PMC6243110 DOI: 10.3389/fpls.2018.01642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/23/2018] [Indexed: 05/04/2023]
Abstract
The Iberian Peninsula is considered as a secondary center of diversity for the common bean, and the Spanish National Plant Genetic Resources Centre's germplasm bank holds more than 3,000 Spanish accessions of Phaseolus vulgaris L. from which a core collection of 202 landraces has been selected. In order to encourage the use of this abundant resource, this study aimed to characterize genetic diversity, by measuring chemical composition in these core collections (in both the seed coat and cotyledon) using previously developed near infrared spectroscopy models. Crucially, these landraces in question all originated under similar agroclimatic conditions, allowing these field trials to be conducted in a single location without significantly altering the agronomic behavior of individual accessions. Using previously reported data, we also explored the correlations between chemical composition and culinary/sensory traits, as well as possible associations between chemical composition and seed coat color or gene pool (Middle American or Andean). The general Mahalanobis distance was >3 in only 11 of 1,950 estimations, confirming the robustness of the regression models previously developed. Variability was greater in seed coat than in cotyledon compounds and ranges for all compounds were wide: ash 34-94 g/kg, Ca 5-31 g/kg, dietary fiber 554-911 g/kg, Mg 2-4.4 g/kg, uronic acid 95-155 g/kg, protein 192-304 g/kg, starch 339-446 g/kg, amylose 208-291 g/kg, amylopectin 333-482 g/kg, and apparent amylose 241-332 g/kg. Accessions with white seed coats tended to be richer in ash, dietary fiber, uronic acid, and Ca, and accessions of the Middle American gene pool had on average 65% more Ca than the Andean gene pool. Strong genetic correlations were not identified between chemical and culinary/sensory traits. This is particularly positive with regards to plant breeding, as it means that synchronic improvement of nutritional composition and sensory traits is possible. The genetic diversity of chemical composition described in the Spanish core collection of beans therefore represents a promising opportunity to develop cultivars with superior nutritional profiles.
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Affiliation(s)
- Ana Rivera
- Miquel Agustí Foundation, Barcelona, Spain
| | | | - Josep Sabaté
- Miquel Agustí Foundation, Barcelona, Spain
- Department of Agri-Food Engineering and Biotechnology, BarcelonaTech, Universitat Politecnica de Catalunya, Barcelona, Spain
| | | | - Joan Casals
- Miquel Agustí Foundation, Barcelona, Spain
- Department of Agri-Food Engineering and Biotechnology, BarcelonaTech, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Aurora Rull
- Miquel Agustí Foundation, Barcelona, Spain
- Department of Agri-Food Engineering and Biotechnology, BarcelonaTech, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Joan Simó
- Miquel Agustí Foundation, Barcelona, Spain
- Department of Agri-Food Engineering and Biotechnology, BarcelonaTech, Universitat Politecnica de Catalunya, Barcelona, Spain
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Luzuriaga-Neira A, Villacís-Rivas G, Cueva-Castillo F, Escudero-Sánchez G, Ulloa-Nuñez A, Rubilar-Quezada M, Monteiro R, Miller MR, Beja-Pereira A. On the origins and genetic diversity of South American chickens: one step closer. Anim Genet 2017; 48:353-357. [PMID: 28094447 DOI: 10.1111/age.12537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2016] [Indexed: 11/27/2022]
Abstract
Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.
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Affiliation(s)
- A Luzuriaga-Neira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - G Villacís-Rivas
- Centro de Biotecnología, Universidad Nacional de Loja, Pio Jaramillo Alvarado s/n sector La Argelia, 1101, Loja, Ecuador
| | - F Cueva-Castillo
- Centro de Biotecnología, Universidad Nacional de Loja, Pio Jaramillo Alvarado s/n sector La Argelia, 1101, Loja, Ecuador
| | - G Escudero-Sánchez
- Universidad Nacional de Loja, Pio Jaramillo Alvarado s/n sector La Argelia, 1101, Loja, Ecuador
| | - A Ulloa-Nuñez
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Mendez 595, Chillán, Chile
| | - M Rubilar-Quezada
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Mendez 595, Chillán, Chile
| | - R Monteiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - M R Miller
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - A Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal.,Department of Biology, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Porto, Portugal
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25
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Agdzhoyan AT, Balanovska EV, Padyukova AD, Dolinina DO, Kuznetsova MA, Zaporozhchenko VV, Skhalyakho RA, Koshel SM, Zhabagin MK, Yusupov YM, Mustafin KK, Ulyanova MV, Tychinskih ZA, Lavryashina MB, Balanovsky OP. [ Gene pool of Siberian Tatars: Five ways of origin for five subethnic groups]. Mol Biol (Mosk) 2017; 50:978-991. [PMID: 28064314 DOI: 10.7868/s0026898416060021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/25/2016] [Indexed: 11/23/2022]
Abstract
Siberian Tatars form the largest Turkic-speaking ethnic group in Western Siberia. The group has a complex hierarchical system of ethnographically diverse populations. Five subethnic groups of Tobol-Irtysh Siberian Tatars (N = 388 samples) have been analyzed for 50 informative Y-chromosomal SNPs. The subethnic groups have been found to be extremely genetically diverse (FST = 21%), so the Siberian Tatars form one of the strongly differentiated ethnic gene pools in Siberia and Central Asia. Every method employed in our studies indicates that different subethnic groups formed in different ways. The gene pool of Isker-Tobol Tatars descended from the local Siberian indigenous population and an intense, albeit relatively recent gene influx from Northeastern Europe. The gene pool of Yalutorovsky Tatars is determined by the Western Asian genetic component. The subethnic group of Siberian Bukhar Tatars is the closest to the gene pool of the Western Caucasus population. Ishtyak-Tokuz Tatars have preserved the genetic legacy of Paleo-Siberians, which connects them with populations from Southern, Western, and Central Siberia. The gene pool of the most isolated Zabolotny (Yaskolbinsky) Tatars is closest to Ugric peoples of Western Siberia and Samoyeds of the Northern Urals. Only two out of five Siberian Tatar groups studied show partial genetic similarity to other populations calling themselves Tatars: Isker-Tobol Siberian Tatars are slightly similar to Kazan Tatars, and Yalutorovsky Siberian Tatars, to Crimean Tatars. The approach based on the full sequencing of the Y chromosome reveals only a weak (2%) Central Asian genetic trace in the Siberian Tatar gene pool, dated to 900 years ago. Hence, the Mongolian hypothesis of the origin of Siberian Tatars is not supported in genetic perspective.
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Affiliation(s)
- A T Agdzhoyan
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Research Center for Medical Genetics, Russian Academy of Sciences, Moscow, 115478 Russia.,
| | - E V Balanovska
- Research Center for Medical Genetics, Russian Academy of Sciences, Moscow, 115478 Russia
| | | | - D O Dolinina
- Kemerovo State University, Kemerovo, 650043 Russia
| | - M A Kuznetsova
- Research Center for Medical Genetics, Russian Academy of Sciences, Moscow, 115478 Russia
| | - V V Zaporozhchenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Research Center for Medical Genetics, Russian Academy of Sciences, Moscow, 115478 Russia
| | - R A Skhalyakho
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Research Center for Medical Genetics, Russian Academy of Sciences, Moscow, 115478 Russia
| | - S M Koshel
- Moscow State University, Moscow, 119991 Russia
| | - M K Zhabagin
- National Laboratory Astana, Nazarbayev University, Astana, 010017 Kazakhstan
| | - Y M Yusupov
- Institute for Strategic Studies of the Republic of Bashkortostan, Social Cultural and Anthropology Center, Ufa, 450008 Bashkortostan, Russia
| | - Kh Kh Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, 141700 Russia
| | - M V Ulyanova
- Kemerovo State University, Kemerovo, 650043 Russia
| | - Z A Tychinskih
- Mendeleev Tobolsk Pedagogical Institute, branch of the Tyumen State University, Tobolsk, 626152 Russia
| | | | - O P Balanovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Research Center for Medical Genetics, Russian Academy of Sciences, Moscow, 115478 Russia
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26
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Dyomin AG, Danilova MI, Mwacharo JM, Masharsky AE, Panteleev AV, Druzhkova AS, Trifonov VA, Galkina SA. Mitochondrial DNA D-loop haplogroup contributions to the genetic diversity of East European domestic chickens from Russia. J Anim Breed Genet 2016; 134:98-108. [PMID: 27988972 DOI: 10.1111/jbg.12248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/07/2016] [Indexed: 12/22/2022]
Abstract
To elucidate geographical and historical aspects of chicken dispersal across Eastern Europe, we analysed the complete mitochondrial DNA D-loop sequence of 86 representatives from chicken breeds traditionally raised in the territory of the East European Plain (Orloff, Pavlov, Russian White, Yurlov Crower, Uzbek Game and Naked Neck). From the 1231-1232 bp D-loop sequence, 35 variable sites that defined 22 haplotypes were identified in modern chicken. All populations, except Uzbek Game, exhibited high values of haplotype and nucleotide diversity suggesting a wide variation in maternal diversity. Inclusion of mtDNA sequences from other European and Asian countries revealed representatives from this study belonging to haplogroups A, E1 and C1. We also assessed fossil chicken material dated to the 9th-18th century from archaeological sites in Northern and Eastern Europe. Three haplotypes found in the fossil specimens belonged to haplogroup E1, while one sample dated to the 18th century was assigned to the C1 haplogroup. This is the first report of the occurrence of the C1 haplogroup in European chicken populations prior to the 20th century based on the fossil material. These results provide evidence for a relatively recent introduction of all haplotypes other than E1 into the East European chicken gene pool with the significant impact of the C1 haplogroup mainly distributed in Southern China.
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Affiliation(s)
- A G Dyomin
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - M I Danilova
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - J M Mwacharo
- Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - A E Masharsky
- Research Resource Centre for Molecular and Cell Technologies, Saint Petersburg State University, Saint Petersburg, Russia
| | - A V Panteleev
- The Ornithology Department, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - A S Druzhkova
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V A Trifonov
- Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S A Galkina
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
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27
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Zelenin AV, Rodionov AV, Bolsheva NL, Badaeva ED, Muravenko OV. [Genome: Origins and evolution of the term]. Mol Biol (Mosk) 2016; 50:611-620. [PMID: 27668601 DOI: 10.7868/s0026898416040170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 11/23/2022]
Abstract
The appearance of a new scientific term is a significant event in the human cognitive process and the result of the realization of the separateness of an object or a phenomenon. Our article concentrates on the origins of basic genetic terms, such as genetics, gene, genotype, genome, gene pool, and genomics. We propose using the term karyogenomics for the special direction of genomics related to the study of the organization and evolution of eukaryotic genomes by means of modern chromosome analysis, as well as by full genome sequencing.
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Affiliation(s)
- A V Zelenin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A V Rodionov
- Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, 197376 Russia.,St. Petersburg State University, St. Petersburg, 199034 Russia.,
| | - N L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E D Badaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - O V Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
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28
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Pollett S, Nelson MI, Kasper M, Tinoco Y, Simons M, Romero C, Silva M, Lin X, Halpin RA, Fedorova N, Stockwell TB, Wentworth D, Holmes EC, Bausch DG. Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012. Emerg Infect Dis 2016. [PMID: 26196599 PMCID: PMC4517729 DOI: 10.3201/eid2108.150084] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
It remains unclear whether lineages of influenza A(H3N2) virus can persist in the tropics and seed temperate areas. We used viral gene sequence data sampled from Peru to test this source-sink model for a Latin American country. Viruses were obtained during 2010-2012 from influenza surveillance cohorts in Cusco, Tumbes, Puerto Maldonado, and Lima. Specimens positive for influenza A(H3N2) virus were randomly selected and underwent hemagglutinin sequencing and phylogeographic analyses. Analysis of 389 hemagglutinin sequences from Peru and 2,192 global sequences demonstrated interseasonal extinction of Peruvian lineages. Extensive mixing occurred with global clades, but some spatial structure was observed at all sites; this structure was weakest in Lima and Puerto Maldonado, indicating that these locations may experience greater viral traffic. The broad diversity and co-circulation of many simultaneous lineages of H3N2 virus in Peru suggests that this country should not be overlooked as a potential source for novel pandemic strains.
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