Mapping the major quantitative trait loci of the heading date trait in Qingke barley (Hordeum vulgare L.) from the Qinghai-Tibetan Plateau via genotyping by sequencing

References

• Börner A, Buck-Sorlin GH, Hayes PM, Malyshev S, Korzun V. 2002. Molecular mapping of major genes and quantitative trait loci determining flowering time in response to photoperiod in barley. Plant Breed. 121(2):129–132.
   Web of Science ®Google Scholar
• Boss PK, Bastow RM, Mylne JS, Dean C. 2004. Multiple pathways in the decision to flower: enabling, promoting, and resetting. Plant Cell. 16(Supp1):S18–S31.
   Google Scholar
• Dai F, Wang X, Zhang XQ, Chen ZH, Nevo E, Jin GL, Wu DZ, Li CD, Zhang GP. 2018. Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley. Plant Biotechnol J. 16(3):760–770.
   Web of Science ®Google Scholar
• Decousset L, Griffiths S, Dunford RP, Pratchett N, Laurie DA. 2000. Development of STS markers closely linked to the Ppd-H1 photoperiod response gene of barley (Hordeum vulgare L.). Theor Appl Genet. 101(8):1202–1206.
   Web of Science ®Google Scholar
• Dondup D. 2015. Haplotypes and Phenotypic Association Analysis of Vernalization and Photoperiod Genes in Chinese Barley. PhD thesis, Chinese Academy of Agricultural Sciences. Beijing.
   Google Scholar
• Dondup D, Dong G, Xu DD, Zhang LS, Zha S, Yuan XM, Tashi NM, Zhang J, Guo GG. 2016. Allelic variation and geographic distribution of vernalization genes HvVRN1 and HvVRN2 in Chinese barley germplasm. Mol Breed. 36(1):11.
   Web of Science ®Google Scholar
• Dong XC, Cheng ZY, Cheng SH, Xu F, An YR, Bian XZ, Chen T. 2011. Identification, characterization, and expression analysis of the TaNF-YB3 gene from Triticum aestivum. Notulae Botanicae Horti Agrobotanici Cluj-Napoca. 39(2):254–263.
   Web of Science ®Google Scholar
• Fu DL, Szűcs P, Yan LL, Helguera M, Skinner JS, von Zitzewitz J, Hayes PM, Dubcovsky J. 2005. Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Genet Genomics. 273(1):54–65.
   PubMed Web of Science ®Google Scholar
• Goffinet B, Gerber S. 2000. Quantitative trait loci: a meta-analysis. Genetics. 155(1):463–473.
   PubMed Web of Science ®Google Scholar
• Hosseini M, Houshmand S, Mohamadi S, Tarang A, Khodambashi M, Rahimsoroush H. 2012. Detection of QTL with main, epistatic and QTL × environment interaction effects for rice grain appearance quality traits using two populations of backcross inbred lines (BILs). Field Crops Res. 135:97–106.
   Web of Science ®Google Scholar
• Karsai I, Szűcs P, Mészáros K, Filichkina T, Hayes PM, Skinner JS, Láng L, Bedő Z. 2005. The Vrn-H2 locus is a major determinant of flowering time in a facultative×winter growth habit barley (Hordeum vulgare L.) mapping population. Theor Appl Genet. 110(8):1458–1466.
   Web of Science ®Google Scholar
• Koebner RMD, Powell W, Donini P. 2001. Contributions of DNA molecular marker technologies to the genetics and breeding of wheat and barley. Plant Breed Rev. 21:181–220.
   Google Scholar
• Kumimoto RW, Adam L, Hymus GJ, Repetti PP, Reuber TL, Marion CM, Hempel FD, Ratcliffe OJ. 2008. The nuclear factor Y subunits NF-YB2 and NF-YB3 play additive roles in the promotion of flowering by inductive long-day photoperiods in Arabidopsis. Planta. 228(5):709–723.
   Web of Science ®Google Scholar
• Lateef DD. 2015. DNA marker technologies in plants and applications for crop improvements. J Biosciences Medicines. 3(05):7–18.
   Google Scholar
• Laurie DA, Pratchett N, Snape JW, Bezant JH. 1995. RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter× spring barley (Hordeum vulgare L.) cross. Genome. 38(3):575–585.
   Web of Science ®Google Scholar
• Li H, Durbin R. 2019. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25(14):1754–1760.
   Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. 1000 genome Project data processing subgroup. 2009. The sequence alignment/map format and samtools. Bioinformatics. 25(16):2078–2079.
   PubMed Web of Science ®Google Scholar
• Liang MX, Hole D, Wu JX, Blake T, Wu YJ. 2012. Expression and functional analysis of NUCLEAR FACTOR-Y, subunit B genes in barley. Planta. 235(4):779–791.
   Web of Science ®Google Scholar
• Liu RH, Meng JL. 2003. Mapdraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data. Hereditas. 25(3):317–321.
   Google Scholar
• Maurer A, Draba V, Jiang Y, Schnaithmann F, Sharma R, Schumann E, Kilian B, Reif JC, Pillen K. 2015. Modelling the genetic architecture of flowering time control in barley through nested association mapping. BMC Genomics. 16(1):290.
   Google Scholar
• McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20(9):1297–1303.
   PubMed Web of Science ®Google Scholar
• Miedaner T, Korzun V. 2012. Marker-assisted selection for disease resistance in wheat and barley breeding. Phytopathology. 102(6):560–566.
   PubMed Web of Science ®Google Scholar
• Nitcher R, Distelfeld A, Tan CT, Yan LL, Dubcovsky J. 2013. Increased copy number at the HvFT1 locus is associated with accelerated flowering time in barley. Mol Genet Genomics. 288(5):261–275.
   Web of Science ®Google Scholar
• Pauli D, Muehlbauer GJ, Smith KP, Cooper B, Hole D, Obert DE, Ullrich SE, Blake TK. 2014. Association mapping of agronomic QTLs in US spring barley breeding germplasm. Plant Genome. 7(3):1–15.
   Web of Science ®Google Scholar
• Poland JA, Brown PJ, Sorrells ME, Jannink JL. 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PloS one. 7(2):e32253.
   PubMed Web of Science ®Google Scholar
• Qiang XL, Chi DZ, Feng JL. 2008. Current situation of highland barley production and development in Qinghai-Tibet Plateau region. Tibet Science and Technology. 3:11–17.
   Google Scholar
• Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, et al. 2014. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 46(7):07–713.
   Web of Science ®Google Scholar
• Sun CH, Deng XJ, Fang J, Chu CC. 2007. An overview of flowering transition in higher plants. Hereditas. 29(10):1182–1190.
   Google Scholar
• Tranquilli G, Dubcovsky J. 2000. Epistatic interaction between vernalization genes Vrn-Am1 and Vrn-Am2 in diploid wheat. J Hered. 91(4):304–306.
   Web of Science ®Google Scholar
• Turner A, Beales J, Faure S, Dunford RP, Laurie DA. 2005. The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science. 310(5750):1031–1034.
   PubMed Web of Science ®Google Scholar
• Van Ooijen JW. 2006. JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen. 33(10.1371).
   Google Scholar
• Wang HY, Smith KP, Combs E, Blake T, Horsley RD, Muehlbauer GJ. 2012. Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm. Theor Appl Genet. 124(1):111–124.
   Web of Science ®Google Scholar
• Wang LH, Yu S, Tong CB, Zhao YZ, Liu Y, Song C, Zhang YX, Zhang XD, Wang Y, Hua W, et al. 2014. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol. 15(2):1–13.
   Web of Science ®Google Scholar
• Wei XJ, Xu JF, Guo HN, Jiang L, Chen SH, Yu CY, Zhou ZL, Hu PS, Zhai HQ, Wan JM. 2010. DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol. 153(4):1747–1758.
   PubMed Web of Science ®Google Scholar
• Wu KL, Yao XH, Yao YH, Bai YX, Chi DZ. 2018. Reflections and practice on breeding barley varieties under the background of diversified uses. Tibet J Agricultural Sciences. 40(S1):1–2.
   Google Scholar
• Xia TF, Zhang LQ, Xu JQ, Wang L, Liu BL, Hao M, Chang X, Zhang TW, Li SM, Zhang HG, et al. 2017. The alternative splicing of EAM8 contributes to early flowering and short-season adaptation in a landrace barley from the Qinghai-Tibetan plateau. Theor Appl Genet. 130(4):757–766.
   Web of Science ®Google Scholar
• Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J. 2006. The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci USA. 103(51):19581–19586.
   Web of Science ®Google Scholar
• Yan WH, Wang P, Chen HX, Zhou HJ, Li QP, Wang CR, Ding ZH, Zhang YS, Yu SB, Xing YZ, Zhang QF. 2011. A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant. 4(2):319–330.
   PubMed Web of Science ®Google Scholar
• Yasuda S. 1989. Differences in mechanism of early maturity between cultivated common wheat and barley. Japan J Breed. 39(3):327–335.
   Google Scholar
• Zang JWK, Chen ZDJQ, Zhao GH. 2004. Applications of barley and study on its components. China Food Additives. 4:43–46.
   Google Scholar
• Zeng XQ, Guo Y, Xu QJ, Mascher M, Guo GG, Li SC, Mao LK, Liu QF, Xia ZF, Zhou JH, et al. 2018. Origin and evolution of qingke barley in Tibet. Nat Commun. 9(1):5433.
   Google Scholar