Scientia Agricultura Sinica ›› 2016, Vol. 49 ›› Issue (11): 2039-2048.doi: 10.3864/j.issn.0578-1752.2016.11.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS •     Next Articles

Genome-Wide Identification of Glyco-hydro-16 Family in Maize and Differentiation Analysis

LIN Feng1,2, GE Min1, ZHOU Ling1, ZHAO Han1   

  1. 1Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences/Provincial Key Laboratory of Agrobiology, Nanjing 210014
    2 Shanghai Key Laboratory of Bio-Energy Crops, Shanghai 200444
  • Received:2016-02-22 Online:2016-06-01 Published:2016-06-01

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Abstract: 【Objective】Genome-wide identification was carried out for Glycoside hydrolase family 16 in maize, and their expression profile across tissues and differentiation between heterotic groups were analyzed. 【Method】Based on the maize V3 sequences, genome-wide survey of Glycoside hydrolase family 16 was conducted according to conserved sequences and domains through hmmersearch program. Blast2GO was used for gene annotation and phylogenetic relationships were analyzed through protein sequences. Expression profiles were examined within the whole transcriptome context at different tissues across development stages in B73. In line with the chromosome locations of the family genes, the authors screened the SNP markers and analyzed their genetic differentiation in different heterotic groups. 【Result】Totally 34 genes were identified in maize throughout genome-wide survey and annotated as xyloglucan endotransglucosylase with 3 conserved motifs discovered in all members. According to the phylogenetic relationships and sequence similarity they were divided into 8 subgroups. Glycoside hydrolase family 16 members were conserved in Gramineae, however, most maize members were not closely related with other Gramineae plants except only 3 members (AC210669.3, GRMZM2G413006, and GRMZM2G166944). The family genes in maize distributed on almost all chromosomes except on chromosomes 3 and 6 with several genes clustered on chromosomes 2, 5 and 10. Different expression profiles across tissues indicated their diversity functions. According to their chromosome location, the authors screened the SNP markers and calculated the genetic differentiation coefficient between the heterotic groups SS and NSS. Ten genes in Glycoside hydrolase family 16 differentiated significantly between the two heterotic groups, distributing on chromosomes 1, 2, 4, 5, 7 and 9. The one on chromosome 2 corresponding to GRMZM2G091118 got the highest Fst 0.52, indicating possible role contribute to heterosis. 【Conclusion】Based on the V3 sequences of maize, 34 genes were identified for Glycoside hydrolase family 16 and annotated as xyloglucan endotransglycosylase. Their expression profiles were different across tissues implying diversity functions. Some family members differentiated significantly between heterotic groups SS and NSS.

Key words: maize, Glyco-hydro-16, gene family, heterotic groups, RNA-seq

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