title: A new allele of acid soil tolerance gene from a malting barley variety.
abstract: BACKGROUND
  Acid soil is a serious limitation to crop production all over the world. Toxic aluminium (Al) cations in acid soil inhibit root growth and reduce yield. Although a gene tolerant to acid soil has been identified, it has not been used in malting barley breeding, which is partly due to the acid soil tolerance gene being linked to unfavorable malting quality traits.
  
  
  RESULTS
  A Brazilian malting barley variety Br2 was identified as tolerant to acid soil. A doubled haploid (DH) population was developed from a cross between Br2 and the Australian acid-sensitive cultivar Hamelin. The DH population was tested for acid soil tolerance in native acid soil and a hydroponic system with pH 4.2, pH 4.2 + Al or pH 6.5, and genotyped using SSR, DArT and gene-specific markers. A single QTL was detected for all parameters related to acid soil tolerance. The QTL was mapped to the known HvMATE location on chromosome 4H. Sequence alignment of the HvMATE gene identified 13 INDELs and 87 SNPs, where one SNP coded for a single amino acid difference between the two varieties. A gene-specific marker was developed to detect the single nucleotide polymorphism between Hamelin and Br2. This marker co-segregated with aluminium tolerance and accounted for 79 % of phenotypic variation for acid soil tolerance.
  
  
  CONCLUSIONS
  The present study identified a novel source of acid soil/Al tolerance from a Brazilian malting barley cultivar Br2. This variety tolerated Al toxicity but was sensitive to low pH which is similar to most other Al-tolerant varieties. A gene-specific marker Cit7 was developed based on the HvMATE gene sequence. Cit7 will improve the efficiency of molecular-assisted selection of new barley varieties with tolerance to acid soil. Multiple alleles exist for the acid soil tolerance gene on chromosome 4H, so a malting barley variety that tolerates acid soil could be developed by selecting suitable tolerant alleles. Tolerance to low pH may play an important role for barley to adapt to acid soils.
authors.affiliation: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. bianmiao2010@gmail.com.|Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia. bianmiao2010@gmail.com.
authors.forename: Miao
authors.initials: M
authors.lastname: Bian
authors.affiliation: Agronomy Department, Zhejiang University, Hangzhou, China. jinxl@zju.edu.cn.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Jin
authors.affiliation: Department of Agriculture & Food WA, 3 Baron-Hay Court, South Perth, WA, 6155, Australia. sue.broughton@agric.wa.gov.au.
authors.forename: Sue
authors.initials: S
authors.lastname: Broughton
authors.affiliation: Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia. xiao-qi.zhang@murdoch.edu.au.
authors.forename: Xiao-Qi
authors.initials: XQ
authors.lastname: Zhang
authors.affiliation: Department of Agriculture & Food WA, 3 Baron-Hay Court, South Perth, WA, 6155, Australia. gaofeng.zhou@agric.wa.gov.au.
authors.forename: Gaofeng
authors.initials: G
authors.lastname: Zhou
authors.affiliation: Tasmanian Institute of Agriculture, University of Tasmania, P.O. Box 46, Kings Meadows, TAS, 7249, Australia. meixue.zhou@utas.edu.au.
authors.forename: Meixue
authors.initials: M
authors.lastname: Zhou
authors.affiliation: Agronomy Department, Zhejiang University, Hangzhou, China. zhanggp@zju.edu.cn.
authors.forename: Guoping
authors.initials: G
authors.lastname: Zhang
authors.affiliation: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. sundongfa@mail.hzau.edu.cn.
authors.forename: Dongfa
authors.initials: D
authors.lastname: Sun
authors.affiliation: Department of Agriculture & Food WA, 3 Baron-Hay Court, South Perth, WA, 6155, Australia. c.li@murdoch.edu.au.|Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia. c.li@murdoch.edu.au.
authors.forename: Chengdao
authors.initials: C
authors.lastname: Li
mesh_terms: D000483:Alleles; D000535:Aluminum / Q000633:toxicity; D002874:Chromosome Mapping; D019295:Computational Biology; D023061:Gene Order; D017343:Genes, Plant; D056726:Genetic Association Studies; D008040:Genetic Linkage; D005819:Genetic Markers; D001467:Hordeum / Q000235:genetics* / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D010641:Phenotype; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D036226:Seedlings / Q000235:genetics* / Q000378:metabolism*; D012987:Soil / Q000737:chemistry*; D013312:Stress, Physiological
chemical_list: D005819:Genetic Markers; D012987:Soil; D000535:Aluminum