The genetic architecture of prolificacy in maize revealed by association mapping and bulk segregant analysis.
Journal
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
ISSN: 1432-2242
Titre abrégé: Theor Appl Genet
Pays: Germany
ID NLM: 0145600
Informations de publication
Date de publication:
09 Aug 2023
09 Aug 2023
Historique:
received:
15
05
2023
accepted:
26
06
2023
medline:
10
8
2023
pubmed:
9
8
2023
entrez:
9
8
2023
Statut:
epublish
Résumé
Here, we revealed maize prolificacy highly correlated with domestication and identified a causal gene ZmEN1 located in one novel QTL qGEN261 that regulating maize prolificacy by using multiple-mapping methods. The development of maize prolificacy (EN) is crucial for enhancing yield and breeding specialty varieties. To achieve this goal, we employed a genome-wide association study (GWAS) to analyze the genetic architecture of EN in maize. Using 492 inbred lines with a wide range of EN variability, our results demonstrated significant differences in genetic, environmental, and interaction effects. The broad-sense heritability (H
Identifiants
pubmed: 37555969
doi: 10.1007/s00122-023-04434-7
pii: 10.1007/s00122-023-04434-7
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
182Subventions
Organisme : National Natural Science Foundation of China
ID : 32171980
Organisme : Henan Provincial Science and Technology Research Project
ID : 232102110181
Organisme : Postdoctoral Research Foundation of China
ID : 2020M682295
Organisme : First-class Postdoctoral Research Grant in Henan Province
ID : 202001032
Organisme : Research Start-up Fund for Youth Talents of Henan Agricultural University
ID : 30500563
Organisme : Open Project Funding of the State Key Laboratory of Crop Stress Adaptation and Improvement
ID : 2021KF07
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Barua D, Mishra A, Kirti PB, Barah P (2022) Identifying Signal-crosstalk mechanism in maize plants during combined salinity and boron stress using integrative systems biology approaches. Biomed Res Int 2022:1027288. https://doi.org/10.1155/2022/1027288
doi: 10.1155/2022/1027288
pubmed: 35505877
pmcid: 9057046
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635. https://doi.org/10.1093/bioinformatics/btm308
doi: 10.1093/bioinformatics/btm308
pubmed: 17586829
Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884–i890. https://doi.org/10.1093/bioinformatics/bty560
doi: 10.1093/bioinformatics/bty560
pubmed: 30423086
pmcid: 6129281
Chen C, Li C, Xie W, Zhang J, Chen W, Ye Z, Liu Y, Long K (2020a) Identification of a novel ZmSBEIIb-interacting protein involved in apparent amylose synthesis. Can J Plant Sci. https://doi.org/10.1139/CJPS-2019-0219
doi: 10.1139/CJPS-2019-0219
Chen Y, Fu Z, Zhang H, Tian R, Yang H, Sun C, Wang L, Zhang W, Guo Z, Zhang X, Tang J (2020b) Cytosolic malate dehydrogenase 4 modulates cellular energetics and storage reserve accumulation in maize endosperm. Plant Biotechnol J 18(12):2420–2435. https://doi.org/10.1111/pbi.13416
doi: 10.1111/pbi.13416
pubmed: 32436613
pmcid: 7680550
Chen L, Luo J, Jin M, Yang N, Liu X, Peng Y, Li W, Phillips A, Cameron B, Bernal JS, Rellán-Álvarez R, Sawers RJH, Liu Q, Yin Y, Ye X, Yan J, Zhang Q, Zhang X, Wu S, Gui S, Wei W, Wang Y, Luo Y, Jiang C, Deng M, Jin M, Jian L, Yu Y, Zhang M, Yang X, Hufford MB, Fernie AR, Warburton ML, Ross-Ibarra J, Yan J (2022a) Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nat Genet 54(11):1736–1745. https://doi.org/10.1038/s41588-022-01184-y
doi: 10.1038/s41588-022-01184-y
pubmed: 36266506
Chen W, Chen L, Zhang X, Yang N, Guo J, Wang M, Ji S, Zhao X, Yin P, Cai L, Xu J, Zhang L, Han Y, Xiao Y, Xu G, Wang Y, Wang S, Wu S, Yang F, Jackson D, Cheng J, Chen S, Sun C, Qin F, Tian F, Fernie AR, Li J, Yan J, Yang X (2022b) Convergent selection of a WD40 protein that enhances grain yield in maize and rice. Science 375(6587):eabg7985. https://doi.org/10.1126/science.abg7985
doi: 10.1126/science.abg7985
pubmed: 35324310
Cui D, Zhao J, Jing Y, Fan M, Liu J, Wang Z, Xin W, Hu Y (2013) The Arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport. PLoS Genet 9(9):e1003759. https://doi.org/10.1371/journal.pgen.1003759
doi: 10.1371/journal.pgen.1003759
pubmed: 24039602
pmcid: 3764202
Duan H, Li J, Sun Y, Xiong X, Sun L, Li W, Gao J, Li N, Zhang J, Cui J, Fu Z, Zhang X, Tang J (2022) Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis. Front Genet 13:1004211. https://doi.org/10.3389/fgene.2022.1004211
doi: 10.3389/fgene.2022.1004211
pubmed: 36437932
pmcid: 9691904
Durieux RP, Kamprath EJ, Moll RH (1993) Yield contribution of apical and subapical ears in prolific and nonprolific corn. Agron J 85(3):606–610. https://doi.org/10.2134/agronj1993.00021962008500030016x
doi: 10.2134/agronj1993.00021962008500030016x
Eugster M, Knaus J, Porzelius C et al (2011) Hands-on tutorial for parallel computing with R. Comput Statistics 26(2):219–239
doi: 10.1007/s00180-010-0206-4
Gelli M, Konda AR, Liu K, Zhang C, Clemente TE, Holding DR, Dweikat IM (2017) Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC Plant Biol 17(1):123. https://doi.org/10.1186/s12870-017-1064-9
doi: 10.1186/s12870-017-1064-9
pubmed: 28697783
pmcid: 5505042
Gong D, Wang Y, Zhang H, Liang K, Sun Q, Qiu F (2023) Overexpression of ZmKL9 increases maize hybrid hundred kernel weight. Plant Biotechnol J 21(3):451–453. https://doi.org/10.1111/pbi.13957
doi: 10.1111/pbi.13957
pubmed: 36331355
Gu X, Huang S, Zhu Z, Ma Y, Yang X, Yao L, Gao X, Zhang M, Liu W, Qiu L, Zhao H, Wang Q, Li Z, Li Z, Meng Q, Yang S, Wang C, Hu X, Ding J (2021) Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean. BMC Plant Biol 21(1):588. https://doi.org/10.1186/s12870-021-03366-y
doi: 10.1186/s12870-021-03366-y
pubmed: 34895144
pmcid: 8665500
Gui S, Wei W, Jiang C, Luo J, Chen L, Wu S, Li W, Wang Y, Li S, Yang N, Li Q, Fernie AR, Yan J (2022) A pan-Zea genome map for enhancing maize improvement. Genome Biol 23(1):178. https://doi.org/10.1186/s13059-022-02742-7
doi: 10.1186/s13059-022-02742-7
pubmed: 35999561
pmcid: 9396798
Han Y, Zhao Q, Tang C, Li Y, Zhang K, Li F, Zhang J (2020) Butyrate mitigates weanling piglets from lipopolysaccharide-induced colitis by regulating microbiota and energy metabolism of the gut-liver axis. Front Microbiol 11:588666. https://doi.org/10.3389/fmicb.2020.588666
doi: 10.3389/fmicb.2020.588666
pubmed: 33363521
pmcid: 7752768
Hannah LC, Giroux M, Boyer C (1993) Biotechnological modification of carbohydrates for sweet corn and maize improvement. Sci Hortic 55(1–2):177–197. https://doi.org/10.1016/0304-4238(93)90031-K
doi: 10.1016/0304-4238(93)90031-K
Hina A, Cao Y, Song S, Li S, Sharmin RA, Elattar MA, Bhat JA, Zhao T (2020) High-resolution mapping in two RIL populations refines major “QTL Hotspot” regions for seed size and shape in soybean (Glycine max L.). Int J Mol Sci 21(3):1040. https://doi.org/10.3390/ijms21031040
doi: 10.3390/ijms21031040
pubmed: 32033213
pmcid: 7038151
Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10(2):156–161. https://doi.org/10.1016/j.pbi.2007.01.003
doi: 10.1016/j.pbi.2007.01.003
pubmed: 17291822
Hong J, Rosental L, Xu Y, Xu D, Orf I, Wang W, Hu Z, Su S, Bai S, Ashraf M, Hu C, Zhang C, Li Z, Xu J, Liu Q, Zhang H, Zhang F, Luo Z, Chen M, Chen X, Betts N, Fernie A, Liang W, Chen G, Brotman Y, Zhang D, Shi J (2023) Genetic architecture of seed glycerolipids in Asian cultivated rice. Plant Cell Environ 46(4):1278–1294. https://doi.org/10.1111/pce.14378
doi: 10.1111/pce.14378
pubmed: 35698268
Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR (2019) An updated gene atlas for maize reveals organ-specific and stress-induced genes. Plant J 97(6):1154–1167. https://doi.org/10.1111/tpj.14184
doi: 10.1111/tpj.14184
pubmed: 30537259
pmcid: 6850026
Hu D, Li X, Yang Z, Liu S, Hao D, Chao M, Zhang J, Yang H, Su X, Jiang M, Lu S, Zhang D, Wang L, Kan G, Wang H, Cheng H, Wang J, Huang F, Tian Z, Yu D (2022) Downregulation of a gibberellin 3β-hydroxylase enhances photosynthesis and increases seed yield in soybean. New Phytol 235(2):502–517. https://doi.org/10.1111/nph.18153
doi: 10.1111/nph.18153
pubmed: 35396723
Huang Y, Wang H, Zhu Y, Huang X, Li S, Wu X, Zhao Y, Bao Z, Qin L, Jin Y, Cui Y, Ma G, Xiao Q, Wang Q, Wang J, Yang X, Liu H, Lu X, Larkins BA, Wang W, Wu Y (2022) THP9 enhances seed protein content and nitrogen-use efficiency in maize. Nature 612(7939):292–300. https://doi.org/10.1038/s41586-022-05441-2
doi: 10.1038/s41586-022-05441-2
pubmed: 36385527
Jia H, Li M, Li W, Liu L, Jian Y, Yang Z, Shen X, Ning Q, Du Y, Zhao R, Jackson D, Yang X, Zhang Z (2020) A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield. Nat Commun 11(1):988. https://doi.org/10.1038/s41467-020-14746-7
doi: 10.1038/s41467-020-14746-7
pubmed: 32080171
pmcid: 7033126
Leni G, Soetemans L, Caligiani A, Sforza S, Bastiaens L (2020) Degree of hydrolysis affects the techno-functional properties of lesser mealworm protein hydrolysates. Foods 9(4):381. https://doi.org/10.3390/foods9040381
doi: 10.3390/foods9040381
pubmed: 32218377
pmcid: 7230224
Li Z, Xu Y (2022) Bulk segregation analysis in the NGS era: a review of its teenage years. Plant J 109(6):1355–1374. https://doi.org/10.1111/tpj.15646
doi: 10.1111/tpj.15646
pubmed: 34931728
Li D, Zhou Z, Lu X, Jiang Y, Li G, Li J, Wang H, Chen S, Li X, Würschum T, Reif JC, Xu S, Li M, Liu W (2021a) Genetic dissection of hybrid performance and heterosis for yield-related traits in maize. Front Plant Sci 12:774478. https://doi.org/10.3389/fpls.2021.774478
doi: 10.3389/fpls.2021.774478
pubmed: 34917109
pmcid: 8670227
Li W, Yu Y, Wang L, Luo Y, Peng Y, Xu Y, Liu X, Wu S, Jian L, Xu J, Xiao Y, Yan J (2021b) The genetic architecture of the dynamic changes in grain moisture in maize. Plant Biotechnol J 19(6):1195–1205. https://doi.org/10.1111/pbi.13541
doi: 10.1111/pbi.13541
pubmed: 33386670
pmcid: 8196655
Li J, Yang H, Xu G, Deng K, Yu J, Xiang S, Zhou K, Zhang Q, Li R, Li M, Ling Y, Yang Z, He G, Zhao F (2022a) QTL analysis of Z414, a chromosome segment substitution line with short, wide grains, and substitution mapping of qGL11 in rice. Rice (n y) 15(1):25. https://doi.org/10.1186/s12284-022-00571-7
doi: 10.1186/s12284-022-00571-7
pubmed: 35532865
Li Z, Chen X, Shi S, Zhang H, Wang X, Chen H, Li W, Li L (2022b) DeepBSA: a deep-learning algorithm improves bulked segregant analysis for dissecting complex traits. Mol Plant 15(9):1418–1427. https://doi.org/10.1016/j.molp.2022.08.004
doi: 10.1016/j.molp.2022.08.004
pubmed: 35996754
Li J, Zhu R, Zhang M, Cao B, Li X, Song B, Liu Z, Wu J (2023a) Natural variations in the PbCPK28 promoter regulate sugar content through interaction with PbTST4 and PbVHA-A1 in pear. Plant J 114(1):124–141. https://doi.org/10.1111/tpj.16126
doi: 10.1111/tpj.16126
pubmed: 36710644
Li K, Tassinari A, Giuliani S, Rosignoli S, Urbany C, Tuberosa R, Salvi S (2023b) QTL mapping identifies novel major loci for kernel row number-associated ear fasciation, ear prolificacy and tillering in maize (Zea mays L.). Front Plant Sci 13:1017983. https://doi.org/10.3389/fpls.2022.1017983
doi: 10.3389/fpls.2022.1017983
pubmed: 36704171
pmcid: 9871824
Li LZ, Xu ZG, Chang TG, Wang L, Kang H, Zhai D, Zhang LY, Zhang P, Liu H, Zhu XG, Wang JW (2023c) Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds. Nat Commun 14(1):290. https://doi.org/10.1038/s41467-023-35966-7
doi: 10.1038/s41467-023-35966-7
pubmed: 36653415
pmcid: 9849336
Liu H, Luo X, Niu L, Xiao Y, Chen L, Liu J, Wang X, Jin M, Li W, Zhang Q, Yan J (2017) Distant eQTLs and non-coding sequences play critical roles in regulating gene expression and quantitative trait variation in maize. Mol Plant 10(3):414–426. https://doi.org/10.1016/j.molp.2016.06.016
doi: 10.1016/j.molp.2016.06.016
pubmed: 27381443
Liu X, Galli M, Camehl I, Gallavotti A (2019) RAMOSA1 ENHANCER LOCUS2-mediated transcriptional repression regulates vegetative and reproductive architecture. Plant Physiol 179(1):348–363. https://doi.org/10.1104/pp.18.00913
doi: 10.1104/pp.18.00913
pubmed: 30348817
Liu Q, Deng S, Liu B, Tao Y, Ai H, Liu J, Zhang Y, Zhao Y, Xu M (2020) A helitron-induced RabGDIα variant causes quantitative recessive resistance to maize rough dwarf disease. Nat Commun 11(1):495. https://doi.org/10.1038/s41467-020-14372-3
doi: 10.1038/s41467-020-14372-3
pubmed: 31980630
pmcid: 6981192
Liu B, Zhang B, Yang Z, Liu Y, Yang S, Shi Y, Jiang C, Qin F (2021a) Manipulating ZmEXPA4 expression ameliorates the drought-induced prolonged anthesis and silking interval in maize. Plant Cell 33(6):2058–2071. https://doi.org/10.1093/plcell/koab083
doi: 10.1093/plcell/koab083
pubmed: 33730156
pmcid: 8290287
Liu JX, Jiang Q, Tao JP, Feng K, Li T, Duan AQ, Wang H, Xu ZS, Liu H, Xiong AS (2021b) Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress. Hortic Res 8(1):262. https://doi.org/10.1038/s41438-021-00707-8
doi: 10.1038/s41438-021-00707-8
pubmed: 34848704
pmcid: 8633011
Liu H, Xiu Z, Yang H, Ma Z, Yang D, Wang H, Tan BC (2022) Maize Shrek1 encodes a WD40 protein that regulates pre-rRNA processing in ribosome biogenesis. Plant Cell 34(10):4028–4044. https://doi.org/10.1093/plcell/koac216
doi: 10.1093/plcell/koac216
pubmed: 35867001
pmcid: 9516035
Lonnquist JH, Peterson CP (1967) Mass selection for prolificacy in maize. Der Züchter 37(4):185–188. https://doi.org/10.1007/bf00329527
doi: 10.1007/bf00329527
Luo B, Ma P, Nie Z, Zhang X, He X, Ding X, Feng X, Lu Q, Ren Z, Lin H, Wu Y, Shen Y, Zhang S, Wu L, Liu D, Pan G, Rong T, Gao S (2019) Metabolite profiling and genome-wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling. Plant J 97(5):947–969. https://doi.org/10.1111/tpj.14160
doi: 10.1111/tpj.14160
pubmed: 30472798
pmcid: 6850195
Luo Y, Zhang M, Liu Y, Liu J, Li W, Chen G, Peng Y, Jin M, Wei W, Jian L, Yan J, Fernie AR, Yan J (2022) Genetic variation in YIGE1 contributes to ear length and grain yield in maize. New Phytol 234(2):513–526. https://doi.org/10.1111/nph.17882
doi: 10.1111/nph.17882
pubmed: 34837389
Lyu J, Huang L, Zhang S, Zhang Y, He W, Zeng P, Zeng Y, Huang G, Zhang J, Ning M, Bao Y, Zhao S, Fu Q, Wade LJ, Chen H, Wang W, Hu F (2020) Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice. Nat Commun 11(1):725. https://doi.org/10.1038/s41467-019-14264-1
doi: 10.1038/s41467-019-14264-1
pubmed: 32024833
pmcid: 7002408
Magwene PM, Willis JH, Kelly JK (2011) The statistics of bulk segregant analysis using next generation sequencing. PLoS Comput Biol 7(11):e1002255. https://doi.org/10.1371/journal.pcbi.1002255
doi: 10.1371/journal.pcbi.1002255
pubmed: 22072954
pmcid: 3207950
Mansfeld BN, Grumet R (2018) QTLseqr: an R package for bulk segregant analysis with next-generation sequencing. Plant Genome. https://doi.org/10.3835/plantgenome2018.01.0006
doi: 10.3835/plantgenome2018.01.0006
pubmed: 30025013
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. https://doi.org/10.1101/gr.107524.110
doi: 10.1101/gr.107524.110
pubmed: 20644199
pmcid: 2928508
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88(21):9828–9832. https://doi.org/10.1073/pnas.88.21.9828
doi: 10.1073/pnas.88.21.9828
pubmed: 1682921
pmcid: 52814
Nasrullah M, Liang L, Rizwanullah M, Yu X, Majrashi A, Alharby HF, Alharbi BM, Fahad S (2022) Estimating nitrogen use efficiency, profitability, and greenhouse gas emission using different methods of fertilization. Front Plant Sci 13:869873. https://doi.org/10.3389/fpls.2022.869873
doi: 10.3389/fpls.2022.869873
pubmed: 35845686
pmcid: 9283998
Nelson OE (1959) Intracistron recombination in the Wx/wx region in maize. Science 130(3378):794–795. https://doi.org/10.1126/science.130.3378.794
doi: 10.1126/science.130.3378.794
pubmed: 17735902
Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2(12):e190. https://doi.org/10.1371/journal.pgen.0020190
doi: 10.1371/journal.pgen.0020190
pubmed: 17194218
pmcid: 1713260
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904–909. https://doi.org/10.1038/ng1847
doi: 10.1038/ng1847
pubmed: 16862161
Qin X, Tian S, Zhang W, Dong X, Ma C, Wang Y, Yan J, Yue B (2021) QDtbn1, an F-box gene affecting maize tassel branch number by a dominant model. Plant Biotechnol J 19(6):1183–1194. https://doi.org/10.1111/pbi.13540
doi: 10.1111/pbi.13540
pubmed: 33382512
pmcid: 8196637
Ren R, Lu X, Han P, Xue C, Lv E, Dong J (2013) Cluster analysis of 27 collections of special maize germplasm resources. J Inner Mong Agric Univ (nat Sci Ed). https://doi.org/10.16853/j.cnki.1009-3575.2013.04.006
doi: 10.16853/j.cnki.1009-3575.2013.04.006
Ren W, Zhao L, Liang J, Wang L, Chen L, Li P, Liu Z, Li X, Zhang Z, Li J, He K, Zhao Z, Ali F, Mi G, Yan J, Zhang F, Chen F, Yuan L, Pan Q (2022) Genome-wide dissection of changes in maize root system architecture during modern breeding. Nat Plants 8(12):1408–1422. https://doi.org/10.1038/s41477-022-01274-z
doi: 10.1038/s41477-022-01274-z
pubmed: 36396706
Rubio-Castillo ÁE, Méndez-Romero JI, Reyes-Díaz R, Santiago-López L, Vallejo-Cordoba B, Hernández-Mendoza A, Sáyago-Ayerdi SG, González-Córdova AF (2021) Tejuino, a traditional fermented beverage: composition, safety quality, and microbial identification. Foods 10(10):2446. https://doi.org/10.3390/foods10102446
doi: 10.3390/foods10102446
pubmed: 34681495
pmcid: 8535997
Russell WA, Eberhart SA (1968) Testcrosses of one- and two-ear types of corn belt maize inbreds. II. Stability of performance in different environments. Crop Sci. https://doi.org/10.2135/cropsci1968.0011183X000800020033x
doi: 10.2135/cropsci1968.0011183X000800020033x
Schmidt P, Hartung J, Rath J, Piepho HP (2019) Estimating broad-sense heritability with unbalanced data from agricultural cultivar trials. Crop Sci. https://doi.org/10.2135/cropsci2018.06.0376
doi: 10.2135/cropsci2018.06.0376
Seckin Dinler B, Cetinkaya H, Secgin Z (2023) The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves. Physiol Mol Biol Plants 29(1):69–85. https://doi.org/10.1007/s12298-022-01269-2
doi: 10.1007/s12298-022-01269-2
pubmed: 36733837
Shen F, Huang Z, Zhang B, Wang Y, Zhang X, Wu T, Xu X, Zhang X, Han Z (2019) Mapping gene markers for apple fruit ring rot disease resistance using a multi-omics approach. G3 (bethesda) 9(5):1663–1678. https://doi.org/10.1534/g3.119.400167
doi: 10.1534/g3.119.400167
pubmed: 30910819
Skibbe DS, Fernandes JF, Medzihradszky KF, Burlingame AL, Walbot V (2009) Mutator transposon activity reprograms the transcriptomes and proteomes of developing maize anthers. Plant J 59(4):622–633. https://doi.org/10.1111/j.1365-313X.2009.03901.x
doi: 10.1111/j.1365-313X.2009.03901.x
pubmed: 19453454
Song J, Shang L, Li C, Wang W, Wang X, Zhang C, Ai G, Ye J, Yang C, Li H, Hong Z, Larkin RM, Ye Z, Zhang J (2022) Variation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip. Nat Commun 13(1):5940. https://doi.org/10.1038/s41467-022-33648-4
doi: 10.1038/s41467-022-33648-4
pubmed: 36209204
pmcid: 9547884
Stelpflug SC, Sekhon RS, Vaillancourt B, Hirsch CN, Buell CR, de Leon N, Kaeppler SM (2016) An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development. Plant Genome. https://doi.org/10.3835/plantgenome2015.04.0025
doi: 10.3835/plantgenome2015.04.0025
pubmed: 27898762
Sun G, Zhang X, Duan H, Gao J, Li N, Su P, Xie H, Li W, Fu Z, Huang Y, Tang J (2022) Dissection of the genetic architecture of peduncle vascular bundle-related traits in maize by a genome-wide association study. Plant Biotechnol J 20(6):1042–1053. https://doi.org/10.1111/pbi.13782
doi: 10.1111/pbi.13782
pubmed: 35080335
pmcid: 9129077
Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74(1):174–183. https://doi.org/10.1111/tpj.12105
doi: 10.1111/tpj.12105
pubmed: 23289725
Tian J, Wang C, Xia J, Wu L, Xu G, Wu W, Li D, Qin W, Han X, Chen Q, Jin W, Tian F (2019) Teosinte ligule allele narrows plant architecture and enhances high-density maize yields. Science 365(6454):658–664. https://doi.org/10.1126/science.aax5482
doi: 10.1126/science.aax5482
pubmed: 31416957
Wang J, Niu B, Huang J, Wang H, Yang X, Dong A, Makaroff C, Ma H, Wang Y (2016) The PHD finger protein MMD1/DUET ensures the progression of male meiotic chromosome condensation and directly regulates the expression of the Condensin gene CAP-D3. Plant Cell 28(8):1894–1909. https://doi.org/10.1105/tpc.16.00040
doi: 10.1105/tpc.16.00040
pubmed: 27385818
pmcid: 5006699
Wang C, Li H, Long Y, Dong Z, Wang J, Liu C, Wei X, Wan X (2023a) A systemic investigation of genetic architecture and gene resources controlling kernel size-related traits in maize. Int J Mol Sci 24(2):1025. https://doi.org/10.3390/ijms24021025
doi: 10.3390/ijms24021025
pubmed: 36674545
pmcid: 9865405
Wang M, Zhang R, Zhao Y et al (2023b) Identifying QTL and candidate genes for prolificacy in maize. Crop J. https://doi.org/10.1016/j.cj.2022.08.007
doi: 10.1016/j.cj.2022.08.007
Wang X, Li Z, Wu J, Zhao M, Wang R, Cao X, Huang M, Liang X (2012) Production, Utilization Status and Development of Special Corn in China. Horticulture & Seed. 2012(10):58–61
Wheeler HE, Shah KP, Brenner J, Garcia T, Aquino-Michaels K, GTEx Consortium, Cox NJ, Nicolae DL, Im HK (2016) Survey of the heritability and sparse architecture of gene expression traits across human tissues. PLoS Genet 12(11):e1006423. https://doi.org/10.1371/journal.pgen.1006423
doi: 10.1371/journal.pgen.1006423
pubmed: 27835642
pmcid: 5106030
Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, Doebley JF (2013) From many, one: genetic control of prolificacy during maize domestication. PLoS Genet 9(6):e1003604. https://doi.org/10.1371/journal.pgen.1003604
doi: 10.1371/journal.pgen.1003604
pubmed: 23825971
pmcid: 3694832
Wosnitza A, Hartmann S (2014) Determination of region-specific data of yield and quality of alternatives to silage maize in fodder crops—field trails with forage gras and clover grass mixtures, Sorghum as well as whole plant silage of grain. Julius-Kühn-Archiv 2014(444):147–182
Wu X, Tang D, Li M, Wang K, Cheng Z (2013) Loose plant architecture1, an INDETERMINATE DOMAIN protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol 161(1):317–329. https://doi.org/10.1104/pp.112.208496
doi: 10.1104/pp.112.208496
pubmed: 23124325
Wu L, Wang P, Wang Y, Cheng Q, Lu Q, Liu J, Li T, Ai Y, Yang W, Sun L, Shen H (2019) Genome-wide correlation of 36 agronomic traits in the 287 pepper (capsicum) accessions obtained from the SLAF-seq-based GWAS. Int J Mol Sci 20(22):5675. https://doi.org/10.3390/ijms20225675
doi: 10.3390/ijms20225675
pubmed: 31766117
pmcid: 6888518
Wyman E, Baker RJ (1991) Estimation of heritability and prediction of selection response in plant populations. Crit Rev Plant Sci 10(3):235–322
doi: 10.1080/07352689109382313
Ye L, Wang Y, Long L, Luo H, Shen Q, Broughton S, Wu D, Shu X, Dai F, Li C, Zhang G (2019) A trypsin family protein gene controls tillering and leaf shape in barley. Plant Physiol 181(2):701–713. https://doi.org/10.1104/pp.19.00717
doi: 10.1104/pp.19.00717
pubmed: 31427466
pmcid: 6776861
Yin L, Zhang H, Tang Z, Xu J, Yin D, Zhang Z, Yuan X, Zhu M, Zhao S, Li X, Liu X (2021) rMVP: a memory-efficient, visualization-enhanced, and parallel-accelerated tool for genome-wide association Study. Genom Proteom Bioinform 19(4):619–628. https://doi.org/10.1016/j.gpb.2020.10.007
doi: 10.1016/j.gpb.2020.10.007
Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38(2):203–208. https://doi.org/10.1038/ng1702
doi: 10.1038/ng1702
pubmed: 16380716
Zhang X, Lin Z, Wang J, Liu H, Zhou L, Zhong S, Li Y, Zhu C, Liu J, Lin Z (2019) The tin1 gene retains the function of promoting tillering in maize. Nat Commun 10(1):5608. https://doi.org/10.1038/s41467-019-13425-6
doi: 10.1038/s41467-019-13425-6
pubmed: 31811145
pmcid: 6898233
Zhang Y, Du H, Xu F, Ding Y, Gui Y, Zhang J, Xu W (2020) Root-bacteria associations boost rhizosheath formation in moderately dry soil through ethylene responses. Plant Physiol 183(2):780–792. https://doi.org/10.1104/pp.19.01020
doi: 10.1104/pp.19.01020
pubmed: 32220965
pmcid: 7271771
Zhang X, Chen S, Shi L, Gong D, Zhang S, Zhao Q, Zhan D, Vasseur L, Wang Y, Yu J, Liao Z, Xu X, Qi R, Wang W, Ma Y, Wang P, Ye N, Ma D, Shi Y, Wang H, Ma X, Kong X, Lin J, Wei L, Ma Y, Li R, Hu G, He H, Zhang L, Ming R, Wang G, Tang H, You M (2021) Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nat Genet 53(8):1250–1259. https://doi.org/10.1038/s41588-021-00895-y
doi: 10.1038/s41588-021-00895-y
pubmed: 34267370
pmcid: 8346365
Zhang A, Jin L, Yarra R, Cao H, Chen P, John Martin JJ (2022a) Transcriptome analysis reveals key developmental and metabolic regulatory aspects of oil palm (Elaeis guineensis Jacq.) during zygotic embryo development. BMC Plant Biol 22(1):112. https://doi.org/10.1186/s12870-022-03459-2
doi: 10.1186/s12870-022-03459-2
pubmed: 35279075
pmcid: 8917659
Zhang L, Qian J, Han Y, Jia Y, Kuang H, Chen J (2022b) Alternative splicing triggered by the insertion of a CACTA transposon attenuates LsGLK and leads to the development of pale-green leaves in lettuce. Plant J 109(1):182–195. https://doi.org/10.1111/tpj.15563
doi: 10.1111/tpj.15563
pubmed: 34724596
Zheng P, Allen WB, Roesler K, Williams ME, Zhang S, Li J, Glassman K, Ranch J, Nubel D, Solawetz W, Bhattramakki D, Llaca V, Deschamps S, Zhong GY, Tarczynski MC, Shen B (2008) A phenylalanine in DGAT is a key determinant of oil content and composition in maize. Nat Genet 40(3):367–372. https://doi.org/10.1038/ng.85
doi: 10.1038/ng.85
pubmed: 18278045
Zhou Q, Fu Z, Li M, Shen Q, Sun C, Feng Y, Liu Y, Jiang J, Qin T, Mao T, Hearne SJ, Wang G, Tang J (2023) Maize tubulin folding cofactor B is required for cell division and cell growth through modulating microtubule homeostasis. New Phytol. https://doi.org/10.1111/nph.18839
doi: 10.1111/nph.18839
pubmed: 37615215
Zhu J, Chen J, Gao F, Xu C, Wu H, Chen K, Si Z, Yan H, Zhang T (2017) Rapid mapping and cloning of the virescent-1 gene in cotton by bulked segregant analysis-next generation sequencing and virus-induced gene silencing strategies. J Exp Bot 68(15):4125–4135. https://doi.org/10.1093/jxb/erx240
doi: 10.1093/jxb/erx240
pubmed: 28922761
pmcid: 5853531