[1] |
Tang CQ, Yang Y, Ohsawa M, Momohara A, Mu J, et al. 2013. Survival of a tertiary relict species, Liriodendron chinense (Magnoliaceae), in southern China, with special reference to village fengshui forests. American Journal of Botany 100:2112−19 doi: 10.3732/ajb.1300057 |
[2] |
Xia H, Si W, Hao Z, Zhong W, Zhu S, et al. 2021. Dynamic changes in the genetic parameters of growth traits with age and their associations with heterosis in hybrid Liriodendron. Tree Genetics & Genomes 17:21 doi: 10.1007/s11295-021-01504-z |
[3] |
Burdon RD, Li Y, Suontama M, Dungey HS. 2017. Genotype × site × silviculture interactions in radiata pine: knowledge, working hypotheses and pointers for research. New Zealand Journal of Forestry Science 47:6 doi: 10.1186/s40490-017-0087-1 |
[4] |
Li Y, Suontama M, Burdon RD, Dungey HS. 2017. Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application. Tree Genetics & Genomes 13:60 doi: 10.1007/s11295-017-1144-x |
[5] |
Xia H, Yang L, Tu Z, Zhang C, Hao Z, et al. 2022. Growth performance and G × E interactions of Liriodendron tulipifera half-sib families across ages in eastern China. European Journal of Forest Research 141:1089−103 doi: 10.1007/s10342-022-01494-0 |
[6] |
Chhetri HB, Macaya-Sanz D, Kainer D, Biswal AK, Evans LM, et al. 2019. Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytologist 223:293−309 doi: 10.1111/nph.15777 |
[7] |
Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, et al. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences of the United States of America 98:11479−84 doi: 10.1073/pnas.201394398 |
[8] |
Fang C, Ma Y, Wu S, Liu Z, Wang Z, et al. 2017. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biology 18:161 doi: 10.1186/s13059-017-1289-9 |
[9] |
Sun P, Jia H, Cheng X, Zhang Y, Li J, et al. 2020. Genetic architecture of leaf morphological and physiological traits in a Populus deltoides 'Danhong' × P. simonii 'Tongliao1' pedigree revealed by quantitative trait locus analysis. Tree Genetics & Genomes 16:45 doi: 10.1007/s11295-020-01438-y |
[10] |
Liu J, Ye M, Zhu S, Jiang L, Sang M, et al. 2018. Two-stage identification of SNP effects on dynamic poplar growth. The Plant Journal 93:286−96 doi: 10.1111/tpj.13777 |
[11] |
Liu P, Bu C, Chen P, El-Kassaby YA, Zhang D, et al. 2023. Enhanced genome-wide association reveals the role of YABBY11-NGATHA-LIKE1 in leaf serration development of Populus. Plant Physiology 191:1702−18 doi: 10.1093/plphys/kiac585 |
[12] |
Freeman JS, Potts BM, Vaillancourt RE. 2008. Few Mendelian genes underlie the quantitative response of a forest tree, Eucalyptus globulus, to a natural fungal epidemic. Genetics 178:563−71 doi: 10.1534/genetics.107.081414 |
[13] |
Kainer D, Padovan A, Degenhardt J, Krause S, Mondal P, et al. 2019. High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus. New Phytologist 223:1489−504 doi: 10.1111/nph.15887 |
[14] |
Müller BSF, De Almeida Filho JE, Lima BM, Garcia CC, Missiaggia A, et al. 2019. Independent and Joint-GWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations. New Phytologist 221:818−33 doi: 10.1111/nph.15449 |
[15] |
Brown GR, Bassoni DL, Gill GP, Fontana JR, Wheeler NC, et al. 2003. Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL verification and candidate gene mapping. Genetics 164:1537−46 doi: 10.1093/genetics/164.4.1537 |
[16] |
De La Torre AR, Puiu D, Crepeau MW, Stevens K, Salzberg SL, et al. 2019. Genomic architecture of complex traits in loblolly pine. New Phytologist 221:1789−801 doi: 10.1111/nph.15535 |
[17] |
Chen Z, Zan Y, Milesi P, Zhou L, Chen J, et al. 2021. Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis. Genome Biology 22:179 doi: 10.1186/s13059-021-02392-1 |
[18] |
Chen J, Hao Z, Guang X, Zhao C, Wang P, et al. 2019. Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation. Nature Plants 5:18−25 doi: 10.1038/s41477-018-0323-6 |
[19] |
Xia H, Hao Z, Shen Y, Tu Z, Yang L, et al. 2023. Genome-wide association study of multiyear dynamic growth traits in hybrid Liriodendron identifies robust genetic loci associated with growth trajectories. The Plant Journal 115:1544−63 doi: 10.1111/tpj.16337 |
[20] |
Hong Y, Zhang M, Zhu J, Zhang Y, Lv C, et al. 2024. Genome-wide association studies reveal novel loci for grain size in two-rowed barley (Hordeum vulgare L.). Theoretical and Applied Genetics 137:58 doi: 10.1007/s00122-024-04562-8 |
[21] |
Xu Z, Zhou Z, Cheng Z, Zhou Y, Wang F, et al. 2023. A transcription factor ZmGLK36 confers broad resistance to maize rough dwarf disease in cereal crops. Nature Plants 9:1720−33 doi: 10.1038/s41477-023-01514-w |
[22] |
Hu J, Chen B, Zhao J, Zhang F, Xie T, et al. 2022. Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding. Nature Genetics 54:694−704 doi: 10.1038/s41588-022-01055-6 |
[23] |
Wang Z, Deng Z, Kong X, Wang F, Guan J, et al. 2022. InDels identification and association analysis with spike and awn length in chinese wheat mini-core collection. International Journal of Molecular Sciences 23:5587 doi: 10.3390/ijms23105587 |
[24] |
Chen S, Zhou Y, Chen Y, Gu J. 2018. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:884−90 doi: 10.1093/bioinformatics/bty560 |
[25] |
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:1297−303 doi: 10.1101/gr.107524.110 |
[26] |
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, et al. 2011. The variant call format and VCFtools. Bioinformatics 27:2156−58 doi: 10.1093/bioinformatics/btr330 |
[27] |
Browning BL, Zhou Y, Browning SR. 2018. A one-penny imputed genome from next-generation reference panels. American Journal of Human Genetics 103:338−48 doi: 10.1016/j.ajhg.2018.07.015 |
[28] |
Wang K, Li M, Hakonarson H. 2010. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38:e164 doi: 10.1093/nar/gkq603 |
[29] |
Lipka AE, Tian F, Wang Q, Peiffer J, Li M, et al. 2012. GAPIT: genome association and prediction integrated tool. Bioinformatics 28:2397−99 doi: 10.1093/bioinformatics/bts444 |
[30] |
Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. 2000. Association mapping in structured populations. American Journal of Human Genetics 67:170−81 doi: 10.1086/302959 |
[31] |
Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, et al. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38:203−08 doi: 10.1038/ng1702 |
[32] |
Guo Y, Long J, He J, Li CI, Cai Q, et al. 2012. Exome sequencing generates high quality data in non-target regions. BMC Genomics 13:194 doi: 10.1186/1471-2164-13-194 |
[33] |
Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y. 2015. Genome measures used for quality control are dependent on gene function and ancestry. Bioinformatics 31:318−23 doi: 10.1093/bioinformatics/btu668 |
[34] |
Wu H, Hao Z, Tu Z, Zong Y, Yang L, et al. 2023. Re-annotation of the Liriodendron chinense genome identifies novel genes and improves genome annotation quality. Tree Genetics & Genomes 19:30 doi: 10.1007/s11295-023-01605-x |
[35] |
Chia JC, Yan J, Ishka MR, Faulkner MM, Simons E, et al. 2023. Loss of OPT3 function decreases phloem copper levels and impairs crosstalk between copper and iron homeostasis and shoot-to-root signaling in Arabidopsis thaliana. The Plant Cell 35:2157−85 doi: 10.1093/plcell/koad053 |
[36] |
Kobayashi T, Nozoye T, Nishizawa NK. 2019. Iron transport and its regulation in plants. Free Radical Biology and Medicine 133:11−20 doi: 10.1016/j.freeradbiomed.2018.10.439 |
[37] |
Wang RX, Wang ZH, Sun YD, Wang LL, Li M, et al. 2024. Molecular mechanism of plant response to copper stress: a review. Environmental and Experimental Botany 218:105590 doi: 10.1016/j.envexpbot.2023.105590 |
[38] |
Ishka MR, Vatamaniuk OK. 2020. Copper deficiency alters shoot architecture and reduces fertility of both gynoecium and androecium in Arabidopsis thaliana. Plant Direct 4:e00288 doi: 10.1002/pld3.288 |
[39] |
Bassham JA. 1962. The path of carbon in photosynthesis. Scientific American 206:89−100 |
[40] |
Carrera DÁ, George GM, Fischer-Stettler M, Galbier F, Eicke S, et al. 2021. Distinct plastid fructose bisphosphate aldolases function in photosynthetic and non-photosynthetic metabolism in Arabidopsis. Journal of Experimental Botany 72:3739−55 doi: 10.1093/jxb/erab099 |
[41] |
Im CH, Hwang SM, Son YS, Heo JB, Bang WY, et al. 2011. Nuclear/Nucleolar GTPase 2 proteins as a subfamily of YlqF/YawG GTPases function in pre-60s ribosomal subunit maturation of mono- and dicotyledonous plants. Journal of Biological Chemistry 286:8620−32 doi: 10.1074/jbc.M110.200816 |
[42] |
Hirschhorn JN, Daly MJ. 2005. Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics 6:95−108 doi: 10.1038/nrg1521 |
[43] |
Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, et al. 2018. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC Plant Biology 18:141 doi: 10.1186/s12870-018-1341-2 |
[44] |
Lin M, Whitmire S, Chen J, Farrel A, Shi X, et al. 2017. Effects of short indels on protein structure and function in human genomes. Scientific Reports 7:9313 doi: 10.1038/s41598-017-09287-x |
[45] |
Yang N, Lu Y, Yang X, Huang J, Zhou Y, et al. 2014. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genetics 10:e1004573 doi: 10.1371/journal.pgen.1004573 |
[46] |
Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, et al. 2010. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42:355−60 doi: 10.1038/ng.546 |
[47] |
Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, et al. 2012. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nature Genetics 44:825−30 doi: 10.1038/ng.2314 |
[48] |
Kobayashi T, Nishizawa NK. 2012. Iron uptake, translocation, and regulation in higher plants. Annual Review of Plant Biology 63:131−52 doi: 10.1146/annurev-arplant-042811-105522 |
[49] |
Zhai Z, Gayomba SR, Jung HI, Vimalakumari NK, Piñeros M, et al. 2014. OPT3 is a phloem-specific iron transporter that is essential for systemic iron signaling and redistribution of iron and cadmium in Arabidopsis. The Plant Cell 26:2249−64 doi: 10.1105/tpc.114.123737 |
[50] |
Cai B, Li Q, Xu Y, Yang L, Bi H, et al. 2016. Genome-wide analysis of the fructose 1,6-bisphosphate aldolase (FBA) gene family and functional characterization of FBA7 in tomato. Plant Physiology and Biochemistry 108:251−65 doi: 10.1016/j.plaphy.2016.07.019 |
[51] |
Uematsu K, Suzuki N, Iwamae T, Inui M, Yukawa H. 2012. Increased fructose 1,6-bisphosphate aldolase in plastids enhances growth and photosynthesis of tobacco plants. Journal of Experimental Botany 63:3001−09 doi: 10.1093/jxb/ers004 |
[52] |
Khanna SM, Taxak PC, Jain PK, Saini R, Srinivasan R. 2014. Glycolytic enzyme activities and gene expression in Cicer arietinum exposed to water-deficit stress. Applied Biochemistry and Biotechnology 173:2241−53 doi: 10.1007/s12010-014-1028-6 |
[53] |
Cai B, Li Q, Liu F, Bi H, Ai X. 2018. Decreasing fructose-1,6-bisphosphate aldolase activity reduces plant growth and tolerance to chilling stress in tomato seedlings. Physiologia Plantarum 163:247−58 doi: 10.1111/ppl.12682 |
[54] |
Lao X, Azuma JI, Sakamoto M. 2013. Two cytosolic aldolases show different expression patterns during shoot elongation in Moso bamboo, Phyllostachys pubescens Mazel. Physiologia Plantarum 149:422−31 doi: 10.1111/ppl.12052 |
[55] |
Haake V, Zrenner R, Sonnewald U, Stitt M. 1998. A moderate decrease of plastid aldolase activity inhibits photosynthesis, alters the levels of sugars and starch, and inhibits growth of potato plants. The Plant Journal 14:147−57 doi: 10.1046/j.1365-313X.1998.00089.x |
[56] |
Niu Q, Liang Y, Zhou J, Dou X, Gao S, et al. 2013. Pollen-expressed transcription factor 2 encodes a novel plant-specific TFIIB-related protein that is required for pollen germination and embryogenesis in Arabidopsis. Molecular Plant 6(4):1091−108 doi: 10.1093/mp/sst083 |