A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality
Identifieur interne : 000819 ( Main/Exploration ); précédent : 000818; suivant : 000820A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality
Auteurs : Rui Sun [République populaire de Chine] ; Yuansheng Chang [République populaire de Chine] ; Fengqiu Yang ; Yi Wang [République populaire de Chine] ; Hui Li [République populaire de Chine] ; Yongbo Zhao ; Dongmei Chen ; Ting Wu [République populaire de Chine] ; Xinzhong Zhang [République populaire de Chine] ; Zhenhai Han [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
Genetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions.
A total of 1733 F1 seedlings derived from ‘Jonathan’ × ‘Golden Delicious’ was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR.
A high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to ‘Jonathan’ with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to ‘Golden Delicious’ with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity.
We demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit quality traits assessed. The candidate genes MDP0000582174 and MDP0000239624 were found to be related to fruit acidity regulation. We conclude that application of RADseq for genetic map construction improved the precision of QTL detection and should be utilized in future studies on the regulatory mechanisms of important fruit traits in apple.
The online version of this article (doi:10.1186/s12864-015-1946-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1946-x
PubMed: 26437648
PubMed Central: 4595315
Affiliations:
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Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Chang, Yuansheng" sort="Chang, Yuansheng" uniqKey="Chang Y" first="Yuansheng" last="Chang">Yuansheng Chang</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Yang, Fengqiu" sort="Yang, Fengqiu" uniqKey="Yang F" first="Fengqiu" last="Yang">Fengqiu Yang</name><affiliation><nlm:aff id="Aff2">Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600 China</nlm:aff><wicri:noCountry code="subfield">Heibei 066600 China</wicri:noCountry></affiliation></author><author><name sortKey="Wang, Yi" sort="Wang, Yi" uniqKey="Wang Y" first="Yi" last="Wang">Yi Wang</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Li, Hui" sort="Li, Hui" uniqKey="Li H" first="Hui" last="Li">Hui Li</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhao, Yongbo" sort="Zhao, Yongbo" uniqKey="Zhao Y" first="Yongbo" last="Zhao">Yongbo Zhao</name><affiliation><nlm:aff id="Aff2">Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600 China</nlm:aff><wicri:noCountry code="subfield">Heibei 066600 China</wicri:noCountry></affiliation></author><author><name sortKey="Chen, Dongmei" sort="Chen, Dongmei" uniqKey="Chen D" first="Dongmei" last="Chen">Dongmei Chen</name><affiliation><nlm:aff id="Aff2">Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600 China</nlm:aff><wicri:noCountry code="subfield">Heibei 066600 China</wicri:noCountry></affiliation></author><author><name sortKey="Wu, Ting" sort="Wu, Ting" uniqKey="Wu T" first="Ting" last="Wu">Ting Wu</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Xinzhong" sort="Zhang, Xinzhong" uniqKey="Zhang X" first="Xinzhong" last="Zhang">Xinzhong Zhang</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Han, Zhenhai" sort="Han, Zhenhai" uniqKey="Han Z" first="Zhenhai" last="Han">Zhenhai Han</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Genetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions.</p></sec><sec><title>Methods</title><p>A total of 1733 F1 seedlings derived from ‘Jonathan’ × ‘Golden Delicious’ was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR.</p></sec><sec><title>Results</title><p>A high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to ‘Jonathan’ with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to ‘Golden Delicious’ with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity.</p></sec><sec><title>Conclusions</title><p>We demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit quality traits assessed. The candidate genes MDP0000582174 and MDP0000239624 were found to be related to fruit acidity regulation. We conclude that application of RADseq for genetic map construction improved the precision of QTL detection and should be utilized in future studies on the regulatory mechanisms of important fruit traits in apple.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1946-x) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Liebhard, R" uniqKey="Liebhard R">R Liebhard</name></author><author><name sortKey="Koller, B" uniqKey="Koller B">B Koller</name></author><author><name sortKey="Gianfranceschi, L" uniqKey="Gianfranceschi L">L Gianfranceschi</name></author><author><name sortKey="Gessler, C" uniqKey="Gessler C">C Gessler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kenis, K" uniqKey="Kenis K">K Kenis</name></author><author><name sortKey="Keulemans, 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Fengqiu" sort="Yang, Fengqiu" uniqKey="Yang F" first="Fengqiu" last="Yang">Fengqiu Yang</name><name sortKey="Zhao, Yongbo" sort="Zhao, Yongbo" uniqKey="Zhao Y" first="Yongbo" last="Zhao">Yongbo Zhao</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Sun, Rui" sort="Sun, Rui" uniqKey="Sun R" first="Rui" last="Sun">Rui Sun</name></noRegion><name sortKey="Chang, Yuansheng" sort="Chang, Yuansheng" uniqKey="Chang Y" first="Yuansheng" last="Chang">Yuansheng Chang</name><name sortKey="Han, Zhenhai" sort="Han, Zhenhai" uniqKey="Han Z" first="Zhenhai" last="Han">Zhenhai Han</name><name sortKey="Li, Hui" sort="Li, Hui" uniqKey="Li H" first="Hui" last="Li">Hui Li</name><name sortKey="Wang, Yi" sort="Wang, Yi" uniqKey="Wang Y" first="Yi" last="Wang">Yi Wang</name><name sortKey="Wu, Ting" sort="Wu, Ting" uniqKey="Wu T" first="Ting" last="Wu">Ting Wu</name><name sortKey="Zhang, Xinzhong" sort="Zhang, Xinzhong" uniqKey="Zhang X" first="Xinzhong" last="Zhang">Xinzhong Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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