Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment
Abstract Background Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
SpringerOpen
2021-06-01
|
| Series: | Rice |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12284-021-00497-6 |
| _version_ | 1831757506727116800 |
|---|---|
| author | Di Cui Cuifeng Tang Hongfeng Lu Jinmei Li Xiaoding Ma Xinxiang A Bing Han Yayun Yang Chao Dong Feifei Zhang Luyuan Dai Longzhi Han |
| author_facet | Di Cui Cuifeng Tang Hongfeng Lu Jinmei Li Xiaoding Ma Xinxiang A Bing Han Yayun Yang Chao Dong Feifei Zhang Luyuan Dai Longzhi Han |
| author_sort | Di Cui |
| collection | DOAJ |
| description | Abstract Background Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing. Results The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Conclusions Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal. |
| first_indexed | 2024-12-22T00:32:37Z |
| format | Article |
| id | doaj.art-e95e04e201ec4921a2de48baf62cf5fe |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-12-22T00:32:37Z |
| publishDate | 2021-06-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-e95e04e201ec4921a2de48baf62cf5fe2022-12-21T18:44:54ZengSpringerOpenRice1939-84251939-84332021-06-0114111410.1186/s12284-021-00497-6Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environmentDi Cui0Cuifeng Tang1Hongfeng Lu2Jinmei Li3Xiaoding Ma4Xinxiang A5Bing Han6Yayun Yang7Chao Dong8Feifei Zhang9Luyuan Dai10Longzhi Han11Institute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural SciencesNovogene Bioinformatics InstituteInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural SciencesInstitute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural SciencesInstitute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural SciencesInstitute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesAbstract Background Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing. Results The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Conclusions Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.https://doi.org/10.1186/s12284-021-00497-6Rice landracesGenetic diversityGenetic differentiationIsolation-by-distanceIsolation-by-environment |
| spellingShingle | Di Cui Cuifeng Tang Hongfeng Lu Jinmei Li Xiaoding Ma Xinxiang A Bing Han Yayun Yang Chao Dong Feifei Zhang Luyuan Dai Longzhi Han Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment Rice Rice landraces Genetic diversity Genetic differentiation Isolation-by-distance Isolation-by-environment |
| title | Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment |
| title_full | Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment |
| title_fullStr | Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment |
| title_full_unstemmed | Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment |
| title_short | Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment |
| title_sort | genetic differentiation and restricted gene flow in rice landraces from yunnan china effects of isolation by distance and isolation by environment |
| topic | Rice landraces Genetic diversity Genetic differentiation Isolation-by-distance Isolation-by-environment |
| url | https://doi.org/10.1186/s12284-021-00497-6 |
| work_keys_str_mv | AT dicui geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT cuifengtang geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT hongfenglu geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT jinmeili geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT xiaodingma geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT xinxianga geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT binghan geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT yayunyang geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT chaodong geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT feifeizhang geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT luyuandai geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment AT longzhihan geneticdifferentiationandrestrictedgeneflowinricelandracesfromyunnanchinaeffectsofisolationbydistanceandisolationbyenvironment |