title: Expression partitioning of homeologs and tandem duplications contribute to salt tolerance in wheat (Triticum aestivum L.).
abstract: Salt stress dramatically reduces crop yield and quality, but the molecular mechanisms underlying salt tolerance remain largely unknown. To explore the wheat transcriptional response to salt stress, we performed high-throughput transcriptome sequencing of 10-day old wheat roots under normal condition and 6, 12, 24 and 48 h after salt stress (HASS) in both a salt-tolerant cultivar and salt-sensitive cultivar. The results demonstrated global gene expression reprogramming with 36,804 genes that were up- or down-regulated in wheat roots under at least one stress condition compared with the controls and revealed the specificity and complexity of the functional pathways between the two cultivars. Further analysis showed that substantial expression partitioning of homeologous wheat genes occurs when the plants are subjected to salt stress, accounting for approximately 63.9% (2,537) and 66.1% (2,624) of the homeologous genes in 'Chinese Spring' (CS) and 'Qing Mai 6' (QM). Interestingly, 143 salt-responsive genes have been duplicated and tandemly arrayed on chromosomes during wheat evolution and polyploidization events, and the expression patterns of 122 (122/143, 85.3%) tandem duplications diverged dynamically over the time-course of salinity exposure. In addition, constitutive expression or silencing of target genes in Arabidopsis and wheat further confirmed our high-confidence salt stress-responsive candidates.
authors.affiliation: Qingdao Agricultural University, Qingdao, 266109, China.
authors.forename: Yumei
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|Northwest A&F University, Yangling, 712100, China.
authors.forename: Zhenshan
authors.initials: Z
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Abul Awlad
authors.initials: AA
authors.lastname: Khan
authors.affiliation: Qingdao Agricultural University, Qingdao, 266109, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Lin
authors.affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Han
authors.affiliation: Qingdao Agricultural University, Qingdao, 266109, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Mu
authors.affiliation: Qingdao Agricultural University, Qingdao, 266109, China.
authors.forename: Yiguo
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Qingdao Agricultural University, Qingdao, 266109, China.
authors.forename: Hongsheng
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Qingdao Agricultural University, Qingdao, 266109, China.
authors.forename: Lingyan
authors.initials: L
authors.lastname: Li
authors.affiliation: Qingdao Agricultural University, Qingdao, 266109, China.
authors.forename: Xianghao
authors.initials: X
authors.lastname: Meng
authors.affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Zhongfu
authors.initials: Z
authors.lastname: Ni
authors.affiliation: State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Xin
mesh_terms: D032461:Chromosomes, Plant; D016000:Cluster Analysis; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D054712:Salinity; D055049:Salt Tolerance / Q000235:genetics*; D013312:Stress, Physiological; D020080:Tandem Repeat Sequences; D059467:Transcriptome; D014908:Triticum / Q000235:genetics* / Q000378:metabolism