|
Adjah K L, Abe A, Adetimirin V O, Asante M D. 2020. Genetic variability, heritability and correlations for milling and grain appearance qualities in some accessions of rice (Oryza sativa L.). Physiology and Molecular Biology of Plants, 26, 1309–1317.
Akinwale M G, Gregorio G, Nwilene F, Akinyele B O, Ogunbayo S A, Odiyi A C. 2011. Heritability and correlation coefficient analysis for yield and its components in rice (Oryza sativa L.). African Journal of Plant Science, 5, 207–212.
Akohoue F, Koch S, Plieske J, Miedaner T. 2022. Separation of the effects of two reduced height (Rht) genes and genomic background to select for less Fusarium head blight of short-strawed winter wheat (Triticum aestivum L.) varieties. TAG Theoretical and Applied Genetics, 135, 4303–4326.
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society (Series B: Methodological), 57, 289–300.
Bone W P, Siewert K M, Jha A, Klarin D, Damrauer S M, Chang K M, Tsao P S, Assimes T L, Ritchie M D, Voight B F. 2021. Multi-trait association studies discover pleiotropic loci between Alzheimer’s disease and cardiometabolic traits. Alzheimer’s Research & Therapy, 13, 1–14.
Carlson M O, Montilla-Bascon G, Hoekenga O A, Tinker N A, Poland J, Baseggio M, Sorrells M E, Jannink J L, Gore M A, Yeats T H. 2019. Multivariate genome-wide association analyses reveal the genetic basis of seed fatty acid composition in oat (Avena sativa L.). G3: Genes, Genomes, Genetics, 9, 2963–2975.
Cui L G, Shan J X, Shi M, Gao J P, Lin H X. 2015. DCA1 acts as a transcriptional co-activator of DST and contributes to drought and salt tolerance in rice. Plos Genetics, 11, e1005617.
Dormatey R, Sun C, Ali K, Coulter J A, Bi Z, Bai J. 2020. Gene pyramiding for sustainable crop improvement against biotic and abiotic stresses. Agronomy, 10, 1255.
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q. 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. TAG Theoretical and Applied Genetics, 112, 1164–1171.
Fan X, Wu J, Chen T, Tie W, Chen H, Zhou F, Lin Y. 2015. Loss-of-function mutation of rice SLAC7 decreases chloroplast stability and induces a photoprotection mechanism in rice. Journal of Integrative Plant Biology, 57, 1063–1077.
He X, Li Z, Guo S, Zheng X, Liu C, Liu Z, Li Y, Yuan Z, Li L. 2023. Epistasis-aware genome-wide association studies provide insights into high-yield and high-quality rice efficient breeding. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2023.07.021.
Hu P, Tan Y, Wen Y, Fang Y, Wang Y, Wu H, Wang J, Wu K, Chai B, Zhu L, Zhang G, Gao Z, Ren D, Zeng D, Shen L, Xue D, Qian Q, Hu J. 2022. LMPA regulates lesion mimic leaf and panicle development through ROS-induced PCD in rice. Frontiers in Plant Science, 13, 875038.
Huang J, Chen Z, Lin J, Guan B, Chen J, Zhang Z, Chen F, Jiang L, Zheng J, Wang T, Chen H, Xie W, Huang S, Wang H, Huang Y, Huang R. 2022. Gw2.1, a new allele of GW2, improves grain weight and grain yield in rice. Plant Science (An International Journal of Experimental Plant Biology), 325, 111495.
Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z. 2013. Genetic bases of rice grain shape: So many genes, so little known. Trends in Plant Science, 18, 218–226.
Huang Y, Zhao S, Fu Y, Sun H, Ma X, Tan L, Liu F, Sun X, Sun H, Gu P, Xie D, Sun C, Zhu Z. 2018. Variation in the regulatory region of FZP causes increases in secondary inflorescence branching and grain yield in rice domestication. The Plant Journal (For Cell and Molecular Biology), 96, 716–733.
Jacquemin J, Bhatia D, Singh K, Wing R A. 2013. The international oryza map alignment project: Development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Current Opinion in Plant Biology, 16, 147–156.
Jaiswal V, Gahlaut V, Meher P K, Mir R R, Jaiswal J P, Rao A R, Balyan H S, Gupta P K. 2016. Genome wide single locus single trait, multi-locus and multi-trait association mapping for some important agronomic traits in common wheat (T. aestivum L.). PLoS ONE, 11, e0159343.
Kanwar P, Sanyal S K, Tokas I, Yadav A K, Pandey A, Kapoor S, Pandey G K. 2014. Comprehensive structural, interaction and expression analysis of CBL and CIPK complement during abiotic stresses and development in rice. Cell Calcium, 56, 81–95.
Klei L, Luca D, Devlin B, Roeder K. 2008. Pleiotropy and principal components of heritability combine to increase power for association analysis. Genetic Epidemiology, 32, 9–19.
Korte A, Vilhjálmsson B J, Segura V, Platt A, Long Q, Nordborg M. 2012. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nature Genetics, 44, 1066–1071.
Li F, Xie J, Zhu X, Wang X, Zhao Y, Ma X, Zhang Z, Rashid M A, Zhang Z, Zhi L, Zhang S, Li J, Li Z, Zhang H. 2018. Genetic basis underlying correlations among growth duration and yield traits revealed by GWAS in rice (Oryza sativa L.). Frontiers in Plant Science, 9, 650.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25, 1754–1760.
Li L, Zheng X, Wang J, Zhang X, He X, Xiong L, Song S, Su J, Diao Y, Yuan Z, Zhang Z, Hu Z. 2023. Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids. Nature Communications, 14, 3930.
Li R, Li M, Ashraf U, Liu S, Zhang J. 2019. Exploring the relationships between yield and yield-related traits for rice varieties released in China from 1978 to 2017. Frontiers in Plant Science, 10, 430305.
Li Y, Wu S, Huang Y, Ma X, Tan L, Liu F, Lv Q, Zhu Z, Hu M, Fu Y, Zhang K, Gu P, Xie D, Sun H, Sun C. 2023. OsMADS17 simultaneously increases grain number and grain weight in rice. Nature Communications, 14, 3098.
Liu Q, Han R, Wu K, Zhang J, Ye Y, Wang S, Chen J, Pan Y, Li Q, Xu X, Zhou J, Tao D, Wu Y, Fu X. 2018. G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nature Communications, 9, 852.
Liu X, Huang M, Fan B, Buckler E S, Zhang Z. 2016. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. Plos Genetics, 12, e1005767.
Liu Z, Hu Y, Du A, Yu L, Fu X, Wu C, Lu L, Liu Y, Wang S, Huang W, Tu S, Ma X, Li H. 2022. Cell wall matrix polysaccharides contribute to salt–alkali tolerance in rice. International Journal of Molecular Sciences, 23, 15019.
Loss Sperandio M V, Santos L A, Huertas Tavares O C, Fernandes M S, De Freitas Lima M, De Souza S R. 2020. Silencing the Oryza sativa plasma membrane H+-ATPase isoform OsA2 affects grain yield and shoot growth and decreases nitrogen concentration. Journal of Plant Physiology, 251, 153220.
Lv C, Lu W, Quan M, Xiao L, Li L, Zhou J, Li P, Zhang D, Du Q. 2021. Pyramiding superior haplotypes and epistatic alleles to accelerate wood quality and yield improvement in poplar breeding. Industrial Crops and Products, 171, 113891.
McCough S R, Doerge R W. 1995. QTL mapping in rice. Trends in Genetics, 11, 482–487.
Nithya N, Beena R, Stephen R, Abida P, Jayalekshmi V, Viji M, Manju R. 2020. Genetic variability, heritability, correlation coefficient and path analysis of morphophysiological and yield related traits of rice under drought stress. Chemical Science Review and Letters, 9, 48–54.
Oladosu Y, Rafii M, Magaji U, Abdullah N, Miah G, Chukwu S C, Hussin G, Ramli A, Kareem I. 2018. Genotypic and phenotypic relationship among yield components in rice under tropical conditions. BioMed Research International, 2018, 8936767.
Pan Y H, Chen L, Guo H F, Feng R, Lou Q J, Rashid M A R, Zhu X Y, Qing D J, Liang H F, Gao L J, Huang C C, Zhao Y, Deng G F. 2022. Systematic analysis of NB-ARC gene family in rice and functional characterization of GNP12. Frontiers in Genetics, 13, 887217.
Qi J, Li J, Han X, Li R, Wu J, Yu H, Hu L, Xiao Y, Lu J, Lou Y. 2016. Jasmonic acid carboxyl methyltransferase regulates development and herbivory-induced defense response in rice. Journal of Integrative Plant Biology, 58, 564–576.
Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C. 2008. Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiology, 147, 1947–1959.
Qi P, Lin Y S, Song X J, Shen J B, Huang W, Shan J X, Zhu M Z, Jiang L, Gao J P, Lin H X. 2012. The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Research, 22, 1666–1680.
Rashid M A R, Zhao Y, Azeem F, Zhao Y, Ahmed H G M D, Atif R M, Pan Y, Zhu X, Liang Y, Zhang H, Li D, Zhang Z, Li Z. 2022. Unveiling the genetic architecture for lodging resistance in rice (Oryza sativa L.) by genome-wide association analyses. Frontiers in Genetics, 13, 960007.
Ren Y, Chen D, Li W, Tao L, Yuan G, Cao Y, Li X, Deng Q, Wang S, Zheng A, Zhu J, Liu H, Wang L, Li P, Li S. 2021. Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding. Journal of Integrative Agriculture, 20, 35–45.
Roberts A, McMillan L, Wang W, Parker J, Rusyn I, Threadgill D. 2007. Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Bioinformatics (Oxford, England), 23, i401-i407.
Ruotsalainen S E, Partanen J J, Cichonska A, Lin J, Benner C, Surakka I, Reeve M P, Palta P, Salmi M, Jalkanen S, Ahola-Olli A, Palotie A, Salomaa V, Daly M J, Pirinen M, Ripatti S, Koskela J. 2021. An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease. European Journal of Human Genetics, 29, 309–324.
Sakamoto T, Matsuoka M. 2008. Identifying and exploiting grain yield genes in rice. Current Opinion in Plant Biology, 11, 209–214.
Schulthess A W, Reif J C, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Ganal M W, Röder M S, Jiang Y. 2017. The roles of pleiotropy and close linkage as revealed by association mapping of yield and correlated traits of wheat (Triticum aestivum L.). Journal of Experimental Botany, 68, 4089–4101.
Shirai Y, Nakanishi Y, Suzuki A, Konaka H, Nishikawa R, Sonehara K, Namba S, Tanaka H, Masuda T, Yaga M, Satoh S, Izumi M, Mizuno Y, Jo T, Maeda Y, Nii T, Oguro-Igashira E, Biobank Japan Project, Morisaki T, et al. 2022. Multi-trait and cross-population genome-wide association studies across autoimmune and allergic diseases identify shared and distinct genetic component. Annals of the Rheumatic Diseases, 81, 1301–1312.
Sinha P, Singh V K, Saxena R K, Khan A W, Abbai R, Chitikineni A, Desai A, Molla J, Upadhyaya H D, Kumar A, Varshney R K. 2020. Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant Biotechnology Journal, 18, 2482–2490.
Van Der Sluis S, Posthuma D, Dolan C V. 2013. TATES: efficient multivariate genotype-phenotype analysis for genome-wide association studies. Plos Genetics, 9, e1003235.
Song X, Meng X, Guo H, Cheng Q, Jing Y, Chen M, Liu G, Wang B, Wang Y, Li J, Yu H. 2022. Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size. Nature Biotechnology, 40, 1403–1411.
Su J, Xu K, Li Z, Hu Y, Hu Z, Zheng X, Song S, Tang Z, Li L. 2021. Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential. Scientific Reports, 11, 6894.
Sui Z, Wang T, Li H, Zhang M, Li Y, Xu R, Xing G, Ni Z, Xin M. 2016. Overexpression of peptide-encoding OsCEP6. 1 results in pleiotropic effects on growth in rice (O. sativa). Frontiers in Plant Science, 7, 228.
Tu D, Jiang Y, Zhang L, Cai M, Li C, Cao C. 2022. Effect of various combinations of temperature during different phenological periods on indica rice yield and quality in the Yangtze River Basin in China. Journal of Integrative Agriculture, 21, 2900–2909.
Wang F, Han T, Song Q, Ye W, Song X, Chu J, Li J, Chen Z J. 2020. The rice circadian clock regulates tiller growth and panicle development through strigolactone signaling and sugar sensing. Plant Cell, 32, 3124–3138.
Wang Q, Tian F, Pan Y, Buckler E S, Zhang Z. 2014. A SUPER powerful method for genome wide association study. PLoS ONE, 9, e107684.
Wu Y P, Chang Y C, Kuo H I, Lin B N, Wang S M, Tseng Y C. 2022. The development of two high-yield and high-quality functional rice cultivars using marker-assisted selection and conventional breeding methods. International Journal of Molecular Sciences, 23, 4678.
Xiao Y, Jiang S, Cheng Q, Wang X, Yan J, Zhang R, Qiao F, Ma C, Luo J, Li W, Liu H, Yang W, Song W, Meng Y, Warburton M L, Zhao J, Wang X, Yan J. 2021. The genetic mechanism of heterosis utilization in maize improvement. Genome Biology, 22, 148.
Xing Y, Zhang Q. 2010. Genetic and molecular bases of rice yield. Annual Review of Plant Biology, 61, 421–442.
Xu H, Toikumo S, Crist R C, Glogowska K, Jinwala Z, Deak J D, Justice A C, Gelernter J, Johnson E C, Kranzler H R, Kember R L. 2023. Identifying genetic loci and phenomic associations of substance use traits: A multi-trait analysis of GWAS (MTAG) study. Addiction, 118, 1942–1952.
Xu P, Li H, Li H, Zhao G, Dai S, Cui X, Liu Z, Shi L, Wang X. 2024. Genome-wide and candidate gene association studies identify BnPAP17 as conferring the utilization of organic phosphorus in oilseed rape. Journal of Integrative Agriculture, 23, 1134–1149.
Yang J, Lee S H, Goddard M E, Visscher P M. 2011. GCTA: A tool for genome-wide complex trait analysis. The American Journal of Human Genetics, 88, 76–82.
Yano K, Yamamoto E, Aya K, Takeuchi H, Lo P C, Hu L, Yamasaki M, Yoshida S, Kitano H, Hirano K, Matsuoka M. 2016. Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nature Genetics, 48, 927–934.
Yu J, Pressoir G, Briggs W H, Vroh B I, Yamasaki M, Doebley J F, McMullen M D, Gaut B S, Nielsen D M, Holland J B, Kresovich S, Buckler E S. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics, 38, 203–208.
Zhang L, Yu H, Ma B, Liu G, Wang J, Wang J, Gao R, Li J, Liu J, Xu J, Zhang Y, Li Q, Huang X, Xu J, Li J, Qian Q, Han B, He Z, Li J. 2017. A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice. Nature Communications, 8, 14789.
Zhang W, Peng K, Cui F, Wang D, Zhao J, Zhang Y, Yu N, Wang Y, Zeng D, Wang Y, Cheng Z, Zhang K. 2021. Cytokinin oxidase/dehydrogenase OsCKX11 coordinates source and sink relationship in rice by simultaneous regulation of leaf senescence and grain number. Plant Biotechnology Journal, 19, 335–350.
Zhou W, Yan L, Fu Z, Guo H, Zhang W, Liu W, Ye Y, Long P. 2023. Increasing planting density and reducing N application improves yield and grain filling at two sowing dates in double-cropping rice systems. Plants, 12, 2298.
Zhou X, Stephens M. 2014. Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nature Methods, 11, 407–409.
|