Abstract
Plant height is vital for crop yield by influencing plant architecture and resistance to lodging. Although lots of quantitative trait loci (QTLs) controlling plant height had been mapped in foxtail millet, their contributions to phenotypic variation were generally small and mapping regions were relatively large, indicating the difficult application in molecular breeding using marker-assisted selection (MAS). In the present paper, a total of 23 QTLs involving in 15 traits were identified via a high-density Bin map containing 3024 Bin markers with an average distance of 0.48 cM through an F2 population. Among them, qPH9, with a large phenotypic variation explained (51.6%) related to plant height, was one of the major QTLs. Furthermore, qPH9 was repeatedly detected in multi-environments under field conditions using two new developed F2 populations from the same F1 plant, and was narrowed down to a smaller interval of 281 kb using 1024 recessive F2 individuals from the same F1 plant. Finally, we found that there was an extremely significant correlation between marker MRI1016 and plant height, and further speculated that Seita.9G088900 and Seita.9G089700 could be key candidates of qPH9. This study laid an important foundation for the cloning of qPH9 and molecular breeding of dwarf varieties via MAS.
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Availability of data and material
Raw sequence data of biparent and 182 F2 individuals are not publicly available due to the research on other important traits, but are available from the corresponding author on reasonable request. The other data generated or analyzed in this study are included in this manuscript and supplementary information files.
Abbreviations
- PH:
-
Plant height
- MPL:
-
Main panicle length
- MPD:
-
Main panicle diameter
- MSD:
-
Main stem diameter
- MPW:
-
Main panicle weight
- MGW:
-
Main grain weight
- FWP:
-
Fresh weight per plant
- SWP:
-
Straw weight per plant
- TGW:
-
Thousand-grain weight
- FLL:
-
Flag leaf length
- FLW:
-
Flag leaf width
- LNT:
-
Leaf number of the tallest tiller
- TN:
-
Tiller number
- NL:
-
Neck length
- BNP:
-
Branch number per panicle
- QTLs:
-
Quantitative trait loci
- MAS:
-
Marker-assisted selection
- PVE:
-
Phenotypic variation explained
- RAD-seq:
-
Restriction site-associated DNA sequencing
- FPKM:
-
Fragments per kilobase million
- SNP:
-
Single nucleotide polymorphism
- InDel:
-
Insertion-deletion
References
Chen DH, Ronald PC (1999) A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Rep 17:53–57
Clouse SD, Langford M, Mcmorris TC (1996) A brassinosteroid-insensitive mutant in Arabidopsis thaliana exhibits multiple defects in growth and development. Plant Physiol 111:671–678
Fang XM, Dong KJ, Wang XQ et al (2016) A high density genetic map and QTL for agronomic and yield traits in foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics 17:336. https://doi.org/10.1186/s12864-016-2628-z
Gao H, Jin MN, Zheng XM et al (2014) Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice. Proc Natl Acad Sci U S A 111:16337–16342. https://doi.org/10.1073/pnas.1418204111
Gooding MJ, Addisu M, Uppal RK, Snape JW, Jones HE (2012) Effect of wheat dwarfing genes on nitrogen-use efficiency. The Journal of Agricultural Science 150:3–22. https://doi.org/10.1017/s0021859611000414
Guan PF, Shen XY, Mu Q et al (2020) Dissection and validation of a QTL cluster linked to Rht-B1 locus controlling grain weight in common wheat (Triticum aestivum L.) using near-isogenic lines. Theor Applied Genet 133:2693–2653. https://doi.org/10.1007/s00122-020-03622-z
Guo EH, Fan HP, Wang XQ, Cheng LP, Wang J, Guo HL, Wang QL (2008) Breeding of new variety Changnong35 in foxtail millet. Chin Agric Sci Bull 24:188–191 ((in Chinese with English summary))
Han YY, Zhang C, Yang HB, Jiao YL (2014) Cytokinin pathway mediates APETALA1 function in the establishment of determinate floral meristems in Arabidopsis. Proc Natl Acad Sci U S A 111:6840–6845. https://doi.org/10.1073/pnas.1318532111
He Q, Zhi H, Tang S et al (2021) QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map. Theor Appl Genet 134:557–572. https://doi.org/10.1007/s00122-020-03714-w
Huang X, Zhao Y, Wei X et al (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39. https://doi.org/10.1038/ng.1018
Hill WG, Zhang XS (2012) On the pleiotropic structure of the genotype-phenotype map and the evolvability of complex organisms. Genetics 190:1131–1137. https://doi.org/10.1534/genetics.111.135681
Itoh H, Ueguchi-Tanaka M, Sentoku N, Kitano H, Matsuoka M, Kobayashi M (2001) Cloning and functional analysis of two gibberellin 3-hydroxylase genes that are differently expressed during the growth of rice. Proc Natl Acad Sci U S A 98:8909–8914. https://doi.org/10.1073/pnas.141239398
Jeon JS, Lee S, Jung KH, Yang WS, Yi GH, Oh BG, An G (2000) Production of transgenic rice plants showing reduced heading date and plant height by ectopic expression of rice MADS-box genes. Mol Breeding 6:581–592
Jiang L, Liu X, Xiong GS et al (2013) (2013) DWARF 53 acts as a repressor of strigolactone signalling in rice. Nature 504:401–405. https://doi.org/10.1038/nature12870
Klein RR, Mullet JE, Jordan DR, Miller FR, Rooney WL, Menz MA, Franks CD, Klein PE (2008) The effect of tropical sorghum conversion and inbred development on genome diversity as revealed by high-resolution genotyping. Crop Science 48:S12–S26. https://doi.org/10.2135/cropsci2007.06.0319tpg
Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Li QQ, Wu GX, Zhao YP, Wang BB, Zhao BB, Kong DX, Wei HB, Chen CX, Wang HY (2020) CRISPR/Cas9-mediated knockout and overexpression studies reveal a role of maize phytochrome C in regulating flowering time and plant height. Plant Biotechnol J 18:2520–2532. https://doi.org/10.1111/pbi.13429
Li MZ, Hao HB, Liu GB, Xie N, Cui HY (2015) Breeding of new summer foxtail millet variety Henggu No.12 with dwarf and eariliest-maturing. Journal of Hebei Agricultural Sciences 19:3–5 ((in Chinese with English summary))
Liu D, Ma C, Hong W, Huang L, Liu M, Liu H, Zeng H, Deng D, Xin H, Song J, Xu C, Hou X, Wang X, Zheng H (2014) Construction and analysis of high-density linkage map using high-throughput sequencing data. Plos One 9:e98855. https://doi.org/10.1371/journal.pone.0098855
Liu TP, He JH, Dong KJ et al (2020) QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica). BMC Genomics 21:141. https://doi.org/10.1186/s12864-020-6553-9
Marklund S, Chaudhary R, Marklund L, Sandberg K, Andersson L (1995) Extensive mtDNA diversity in horses revealed by PCR-SSCP analysis. Anim Genet 26:193–196
Mauro-Herrera M, Doust AN (2016) Development and genetic control of plant architecture and biomass in the panicoid grass. Setaria. Plos One 11:e0151346. https://doi.org/10.1371/journal.pone.0151346
McKenna A, Hanna M, Banks E et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110
Multani DS, Briggs SP, Chamberlin MA, Blakeslee JJ, Murphy AS, Johal GS (2003) Loss of an MDR transporter in compact stalks of Maize br2 and Sorghum dw3 mutants. Science 302:81–84. https://doi.org/10.1126/science.1086072
Onishi K, Horiuchi Y, Ishigoh-Oka N, Takagi K, Ichikawa N, Maruoka M, Yoshio S (2007) A QTL culster for plant architecture and its ecological significance in Asian wild rice. Breed Sci 57:7–16
Ooijen JW. (2004) MapQTL5.0, software for the mapping of quantitative trait loci in experimental populations. Kyazma BV, Wageningen, The Netherlands
Sasaki A, Itoh H, Gomi K, Ueguchi-Tanaka M, Ishiyama K, Dh KMJ, Kitano H, Ashikari M, Matsuoka M (2003) Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science 299:1896–1898. https://doi.org/10.1126/science.1081077
Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai Y-S, Gill BS, Faris JD (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555. https://doi.org/10.1534/genetics.105.044727
Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99:9043–9043. https://doi.org/10.1073/pnas.132266399
Sun TP (2011) The molecular mechanism and evolution of the GA-GID1-DELLA signaling module in plants. Curr Biol 21:R338–R345. https://doi.org/10.1016/j.cub.2011.02.036
Tian BH, Wang JG, Zhang LX, Li YJ, Wang SY, Li HJ (2010) Assessment of resistance to lodging of landrace and improved cultivars in foxtail millet. Euphytica 172:295–302. https://doi.org/10.1007/s10681-009-9999-z
Ueguchi-Tanaka M, Ashikari M, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow TY, Hsing Y, Kitano H, Yamaguchi I (2005) GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437:693–698. https://doi.org/10.1038/nature04028
Van Os H, Stam P, Visser RGF, van Eck HJ (2005) SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor Appl Genet 112(1):187–194. https://doi.org/10.1007/s00122-005-0124-y
Wang J, Wang ZL, Du XF et al (2017) A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq. Plos One 12:e0179717. https://doi.org/10.1371/journal.pone.0179717
Wang J, Zhang X, Lin ZW (2018) QTL mapping in a maize F2 population using Genotyping-by-Sequencing and a modified fine-mapping strategy. Plant Sci 276:171–180. https://doi.org/10.1016/j.plantsci.2018.08.019
Wang ZL, Wang J, Peng JX et al (2019) QTL mapping for 11 agronomic traits based on a genome-wide Bin-map in a large F2 population of foxtail millet (Setaria italica (L.) P. Beauv.). Mol Breeding 39:18. https://doi.org/10.1007/s11032-019-0930-6
Xue CX, Zhi H, Fang XJ, Liu XT, Tang S, Chai Y, Zhao BH, Jia GQ, Diao XM (2016) Characterization and fine mapping of SiDWARF2 (D2) in foxtail millet. Crop Science 56:95–103. https://doi.org/10.2135/cropsci2015.05.0331
Xue WY, Xing YZ, Weng XY, Zhao Y, Tang WJ, Wang L, Zhou HJ, Yu SB, Xu CG, Li XH, Zhang QF (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767. https://doi.org/10.1038/ng.143
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 4:319–330. https://doi.org/10.1093/mp/ssq070
Yang L, Wang HN, Hou XH, Zou YP, Han TS, Niu XM, Zhang J, Zhao Z, Todesco M, Balasubramanian S, Guo YL (2018) Parallel evolution of common allelic variants confers flowering diversity in Capsella rubella. Plant Cell 30:1322–1336. https://doi.org/10.1105/tpc.18.00124
Zhang K, Fan GY, Zhang XX et al (2017) Identification of QTLs for 14 agronomically important traits in Setaria italica based on SNPs generated from high-throughput sequencing. G3 7: 1587–1594. https://doi.org/10.1534/g3.117.041517/-/DC1
Zhao MC, Zhi H, Zhang X, Jia GQ, Diao XM (2019) Retrotransposon-mediated DELLA transcriptional reprograming underlies semi-dominant dwarfism in foxtail millet. The Crop Journal 7:458–468. https://doi.org/10.1016/j.cj.2018.12
Funding
This research was supported by National Key R&D Program of China (2018YFD1000700), National Youth Science Foundation of China (32001609), Minor Crop Molecular Breeding Platform Special Project of Shanxi Academy of Agricultural Sciences (YGC2019FZ3), Research Project Supported by Shanxi Scholarship Council of China (HGKY2019101), Agricultural Science and Technology Innovation Research Project of Shanxi Academy of Agricultural Sciences (YCX2020YQ35), and Research Program Sponsored by Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (202105D121010).
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JW conceived and supervised the complete study; XFD and ZLW performed the experiments and carried out the bioinformatics work; EHG, SCL, KNH, YXL, and LYZ were responsible for the field trial; XFD and JW wrote and revised the manuscript. All authors have read and approved the final manuscript.
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Supplementary Information
Fig. S1
The Bin genetic linkage map based on resequencing strategy in foxtail millet. The X-axis indicated chromosomes; the Y-axis indicated the genetic position of each chromosome (cM) (PNG 32 kb)
Fig. S2
Genetic distance versus physical distance in foxtail millet. The X-axis indicates the genetic position of each chromosome; the Y-axis indicates the physical position of each chromosome; dots indicate the genetic position against the reference physical position (PNG 266 kb)
Fig. S3
Expression analysis of candidates in stems between Henggu12 and Changnong35. ** Means significant difference at the 0.01 probability level (PNG 20 kb)
Fig. S4
Difference of the coding sequence of Seita.9G089700 between Henggu12 and Changnong35 (JPG 1404 kb)
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Du, X., Wang, ·., Han, ·. et al. Fine mapping of qPH9, a major quantitative trait locus, responsible for plant height in foxtail millet [Setaria italica (L.) P. Beauv.]. Mol Breeding 41, 77 (2021). https://doi.org/10.1007/s11032-021-01261-w
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DOI: https://doi.org/10.1007/s11032-021-01261-w