A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit
Abstract Background Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. Results We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of st...
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2021
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oai:doaj.org-article:702874c9b4b1426faf6ca28d833c5c432021-11-14T12:42:45ZA systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit10.1186/s13059-021-02531-81474-760Xhttps://doaj.org/article/702874c9b4b1426faf6ca28d833c5c432021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02531-8https://doaj.org/toc/1474-760XAbstract Background Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. Results We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function of PbrNSC in regulating lignocellulose formation using both pear fruit and Arabidopsis plants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation. Conclusions This study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.Runze WangYongsong XueJing FanJia-Long YaoMengfan QinTao LinQun LianMingyue ZhangXiaolong LiJiaming LiManyi SunBobo SongJiaying ZhangKejiao ZhaoXu ChenHongju HuZhangjun FeiCheng XueJun WuBMCarticlePear fruitCo-expression networkeQTLStone cell formationNAC transcription factorTranscriptional regulationBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-23 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Pear fruit Co-expression network eQTL Stone cell formation NAC transcription factor Transcriptional regulation Biology (General) QH301-705.5 Genetics QH426-470 |
| spellingShingle |
Pear fruit Co-expression network eQTL Stone cell formation NAC transcription factor Transcriptional regulation Biology (General) QH301-705.5 Genetics QH426-470 Runze Wang Yongsong Xue Jing Fan Jia-Long Yao Mengfan Qin Tao Lin Qun Lian Mingyue Zhang Xiaolong Li Jiaming Li Manyi Sun Bobo Song Jiaying Zhang Kejiao Zhao Xu Chen Hongju Hu Zhangjun Fei Cheng Xue Jun Wu A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit |
| description |
Abstract Background Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. Results We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function of PbrNSC in regulating lignocellulose formation using both pear fruit and Arabidopsis plants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation. Conclusions This study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose. |
| format |
article |
| author |
Runze Wang Yongsong Xue Jing Fan Jia-Long Yao Mengfan Qin Tao Lin Qun Lian Mingyue Zhang Xiaolong Li Jiaming Li Manyi Sun Bobo Song Jiaying Zhang Kejiao Zhao Xu Chen Hongju Hu Zhangjun Fei Cheng Xue Jun Wu |
| author_facet |
Runze Wang Yongsong Xue Jing Fan Jia-Long Yao Mengfan Qin Tao Lin Qun Lian Mingyue Zhang Xiaolong Li Jiaming Li Manyi Sun Bobo Song Jiaying Zhang Kejiao Zhao Xu Chen Hongju Hu Zhangjun Fei Cheng Xue Jun Wu |
| author_sort |
Runze Wang |
| title |
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit |
| title_short |
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit |
| title_full |
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit |
| title_fullStr |
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit |
| title_full_unstemmed |
A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit |
| title_sort |
systems genetics approach reveals pbrnsc as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit |
| publisher |
BMC |
| publishDate |
2021 |
| url |
https://doaj.org/article/702874c9b4b1426faf6ca28d833c5c43 |
| work_keys_str_mv |
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