Xiangbo Zhang1, Yang Cui2, Juxuan Wang3, Yonghong Huang1, Yongwen Qi4. 1. Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, 510316, China. 2. Sciences Rice and Sorghum Institude, Sichuan Academy of Agricultural, Deyang, 618000, China. 3. Yunnan Yingmao Sugar Industry (Group) Co. LTD, Kunming, 650228, China. 4. Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, 510316, China. yongwen2001@126.com.
Abstract
BACKGROUND: The biological pathways related to Arabidopsis seed development have been well studied and functional genes involved in it have been discovered. However, functional studies about maize seed development were more limited compared to Arabidopsis. OBJECTIVE: Therefore, transferring knowledge from Arabidopsis into maize would facilitate functional studies about maize seed development. METHOD: In this study, public transcriptome data of the two species related to seed development were obtained. Co-expression network in each species was compared by integrating orthology information. RESULTS: This conserved co-functional network contained 4510 maize and 4808 Arabidopsis genes, respectively. Most of these genes were expressed in throughout embryo, early or later endosperm/seed. These conserved co-functional genes were significantly enriched for members of PPR protein family, which was consistent with that PPR proteins play an important role in maize seed development. Spatial-temporally co-functional genes were discovered in the seed coat and embryo. Furthermore, 66 well-studied genes involved in Arabidopsis seed development were co-functional with 319 maize genes and one maize gene (GRMZM2G036050) was further confirmed using an EMS-induced seed defective mutant by bulked segregating RNA sequencing (BSR) analysis. CONCLUSIONS: Altogether, these results showed the potential of this approach to support functional studies in maize seed development by transferring knowledge from Arabidopsis.
BACKGROUND: The biological pathways related to Arabidopsis seed development have been well studied and functional genes involved in it have been discovered. However, functional studies about maize seed development were more limited compared to Arabidopsis. OBJECTIVE: Therefore, transferring knowledge from Arabidopsis into maize would facilitate functional studies about maize seed development. METHOD: In this study, public transcriptome data of the two species related to seed development were obtained. Co-expression network in each species was compared by integrating orthology information. RESULTS: This conserved co-functional network contained 4510 maize and 4808 Arabidopsis genes, respectively. Most of these genes were expressed in throughout embryo, early or later endosperm/seed. These conserved co-functional genes were significantly enriched for members of PPR protein family, which was consistent with that PPR proteins play an important role in maize seed development. Spatial-temporally co-functional genes were discovered in the seed coat and embryo. Furthermore, 66 well-studied genes involved in Arabidopsis seed development were co-functional with 319 maize genes and one maize gene (GRMZM2G036050) was further confirmed using an EMS-induced seed defective mutant by bulked segregating RNA sequencing (BSR) analysis. CONCLUSIONS: Altogether, these results showed the potential of this approach to support functional studies in maize seed development by transferring knowledge from Arabidopsis.
Authors: H Charles J Godfray; John R Beddington; Ian R Crute; Lawrence Haddad; David Lawrence; James F Muir; Jules Pretty; Sherman Robinson; Sandy M Thomas; Camilla Toulmin Journal: Science Date: 2010-01-28 Impact factor: 47.728
Authors: Song Feng Li; Olga Nicolaou Milliken; Hanh Pham; Reg Seyit; Ross Napoli; Jeremy Preston; Anna M Koltunow; Roger W Parish Journal: Plant Cell Date: 2009-01-09 Impact factor: 11.277
Authors: Yinping Jiao; Paul Peluso; Jinghua Shi; Tiffany Liang; Michelle C Stitzer; Bo Wang; Michael S Campbell; Joshua C Stein; Xuehong Wei; Chen-Shan Chin; Katherine Guill; Michael Regulski; Sunita Kumari; Andrew Olson; Jonathan Gent; Kevin L Schneider; Thomas K Wolfgruber; Michael R May; Nathan M Springer; Eric Antoniou; W Richard McCombie; Gernot G Presting; Michael McMullen; Jeffrey Ross-Ibarra; R Kelly Dawe; Alex Hastie; David R Rank; Doreen Ware Journal: Nature Date: 2017-06-12 Impact factor: 49.962