KRN4 Controls Quantitative Variation in Maize Kernel Row Number

PLoS Genetics

Volumn 11, Issue 11, 2015, Pages

  Liu, Lei ^a   Du, Yanfang ^a   Shen, Xiaomeng ^a   Li, Manfei ^a   Sun, Wei ^a   Huang, Juan ^a   Liu, Zhijie ^a   Tao, Yongsheng ^b   Zheng, Yonglian ^a   Yan, Jianbing ^a   Zhang, Zuxin ^a,c  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b AGRICULTURAL UNIVERSITY OF HEBEI   (China)

^c Hubei Collaborative Innovation Center for Grain Crops   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CONTROLLED STUDY; DOMESTICATION; GENE; GENE EXPRESSION; GENE INSERTION; GENE MAPPING; GENETIC LINKAGE; GENETIC VARIABILITY; GERMPLASM; HAPLOTYPE; KERNEL ROW NUMBER; KRN4 GENE; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT PARAMETERS; PLANT YIELD; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSPOSON; UB3 GENE; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR CLONING; PLANT GENE;

PLANT PROTEIN;

CLONING, MOLECULAR; GENE EXPRESSION PROFILING; GENES, PLANT; PLANT PROTEINS; ZEA MAYS;

EID: 84949293658     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1005670     Document Type: Article

References (48)

1. Doebley J, The genetics of maize evolution. Ann Rev Genet. 2004; 38: 37–59. 15568971
2. Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, et al. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet. 2011; 7:e1002383. doi: 10.1371/journal.pgen.1002383 22125498
3. Lei L, Yanfang D, Dongao H, Man W, Shen X, Bing Y, et al. Genetic architecture of maize kernel row number and whole genome prediction. Theor Appl Genet. 2015.
4. Vollbrecht E, Schmidt RJ, JL Hake, SC Development of the inflorescences. In: Bennetzen, Handbook of Maize: Its Biology, eds New York: Springer; 2009. pp.; 13–40.
5. Bommert P, Lunde C, Nardmann J, Vollbrecht E, Running M, Jackson D, Hake S, Werr W, thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucine-rich repeat receptor-like kinase. Development. 2005; 132: 1235–45. 15716347
6. Taguchi-Shiobara F, Yuan Z, Hake S, Jackson D, The fasciated ear2 gene encodes a leucine-rich repeat receptor-like protein that regulates shoot meristem proliferation in maize. Genes Dev. 2001; 15: 2755–2766. 11641280
7. Bommert P, Nagasawa NS, Jackson D, Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet. 2013; 45(3): 334–337. doi: 10.1038/ng.2534 23377180
8. Bommert P, Je BI, Goldshmidt A, Jackson D, The maize Gα gene COMPACT PLANT2 functions in CLAVATA signalling to control shoot meristem size. Nature. 2013; 502: 555–558. doi: 10.1038/nature12583 24025774
9. McSteen P, Branching out: the ramosa pathway and the evolution of grass inflorescence morphology. Plant Cell. 2006; 18(3): 518–522. 16513602
10. Chuck G, Cigan AM, Saeteurn K, Hake S, The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat Genet. 2007; 39(4): 544–549. 17369828
11. Chuck G, Whipple C, Jackson D, Hake S, The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development. 2010; 137: 1243–1250. doi: 10.1242/dev.048348 20223762
12. Bomblies K1, Doebley JF, Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication. Genetics. 2006; 172: 519–531. 16204211
13. Chuck GS, Brown PJ, Meeley R, Hake S, Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordia initiation. Proc Natl Acad Sci USA. 2014; 111(52): 18775–18780. doi: 10.1073/pnas.1407401112 25512525
14. Yang X, Gao S, Xu S, Zhang Z, Prasanna B M, Li L, et al. Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breed. 2011; 28: 511–526.
15. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2006; 38: 203–208. 16380716
16. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES, TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007; 23: 2633–2635. 17586829
17. Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, et al. The origin of the naked grains of maize. Nature. 2005; 436: 714–719. 16079849
18. Studer A, Zhao Q, Ross-Ibarra J, Doebley J, Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet. 2011; 43: 1160–1163. doi: 10.1038/ng.942 21946354
19. Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet. 2010; 42: 541–545. doi: 10.1038/ng.591 20495565
20. Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, et al. OsSPL14 promotes panicle branching and higher grain productivity in rice. 2010; Nat Genet. 42: 545–549. doi: 10.1038/ng.592 20495564
21. Robbins ML, Sekhon RS, Meeley R, Chopra S, A Mutator transposon insertion is associated with ectopic expression of a tandemly repeated multicopy Myb gene pericarp color1 of maize. Genetics. 2008; 178: 1859–1874.A Mutator transposon insertion is associated with ectopic expression of a tandemly repeated multicopy Myb gene doi: 10.1534/genetics.107.082503 18430921
22. Lu Z, Yu H, Xiong G, Wang J, Jiao Y, Liu G, et al. Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. Plant Cell. 2013; 25: 3743–3759. doi: 10.1105/tpc.113.113639 24170127
23. Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M, et al. The OsTB1 gene negatively regulates lateral branching in rice. Plant J. 2003; 33: 513–520. 12581309
24. Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, et al. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet. 2009; 41: 494–497. doi: 10.1038/ng.352 19305410
25. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci USA. 2007; 104: 11376–11381. 17595297
26. Hung HY, Shannon LM, Tian F, Bradbury PJ, Chen C, Flint-Garcia SA, et al. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc Natl Acad Sci USA. 2012; 109: E1913–1921. doi: 10.1073/pnas.1203189109 22711828
27. Yang Q, Li Z, Li W, Ku L, Wang C, Ye J, et al. CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. Proc Natl Acad Sci USA. 2013; 110: 16969–16974. doi: 10.1073/pnas.1310949110 24089449
28. Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, et al. From Many, One: Genetic Control of Prolificacy during Maize Domestication. PLoS Genet. 2013; 9(6): e1003604. doi: 10.1371/journal.pgen.1003604 23825971
29. Arteaga-Vazquez M, Sidorenko L, Rabanal FA, Shrivistava R, Nobuta K, Green PJ, et al. RNA-mediated trans-communication can establish paramutation at the b1 locus in maize. Proc Natl Acad Sci U S A. 2010; 107(29): 12986–91. doi: 10.1073/pnas.1007972107 20616013
30. Doebley JF, Gaut BS, Smith BD, The molecular genetics of crop domestication. Cell. 2006; 127: 1309–1321. 17190597
31. Li H, Peng Z, Yang X, Wang W, Fu J, Wang J, et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet. 2013; 45: 43–50. doi: 10.1038/ng.2484 23242369
32. SAS Institute2001. SAS/STAT User’s Guide v. 8.2. SAS Institute, Cary, N.C.,
33. Barrett JC, Fry B, Maller J, Daly MJ, Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics. 2005; 21: 263–5. 15297300
34. Paterson AH, DeVerna JW, Lanini B, Tanksley SD, Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics. 1990; 124:735–742. 1968874
35. McCarty DR, Settles AM, Suzuki M, Tan BC, Latshaw S, Porch T, et al. Steady-state transposon mutagenesis in inbred maize. Plant J. 2005; 44: 52–61. 16167895
36. Wen W, Franco J, Chavez-Tovar VH, Yan J, Taba S, Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement. PLoS One. 2012;7(3):e32626. doi: 10.1371/journal.pone.0032626 22412898
37. Librado P, Rozas J, DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25: 1451–1452. doi: 10.1093/bioinformatics/btp187 19346325
38. Eyre Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS, Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci U S A. 1998; 95: 4441–4446. 9539756
39. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS, Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci U S A. 2001;98: 9161–9166. 11470895
40. Tenaillon MI, U’Ren J, Tenaillon O, Gaut BS, Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol. 2004; 21: 1214–25. 15014173
41. White SE, Doebley JF, The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics. 1999; 153: 1455–1462. 10545473
42. Hudson RR, And MK, Aguadé M, A Test of Neutral Molecular Evolution Based on Nucleotide Data. Genetics. 1987; 116: 153–159. 3110004
43. Yang Z, Wang X, Gu S, Hu Z, Xu H, Xu C, Comparative study of SBP-box gene family in Arabidopsis and rice. Gene. 2008; 407: 1–11. 17629421
44. Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, et al. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010; 463: 763–768. doi: 10.1038/nature08747 20148030
45. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009; 457: 551–556. doi: 10.1038/nature07723 19189423
46. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, et al. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science. 2002; 296: 92–100. 11935018
47. Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, et al. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol. 2012; 30: 549–554. doi: 10.1038/nbt.2195 22580950
48. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009; 326: 1112–1115. doi: 10.1126/science.1178534 19965430