Arcade, A., Labourdette, A., Falque, M., Mangin, B., Chardon, F., Charcosset, A., & Joets, J. (2004). BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics, 20(14), 2324-2326.
Arifuzzaman, M., Sayed, M.A., Muzammil, S., Pillen, K., Schumann, H., Naz, A. A., & Léon, J. (2014). Detection and validation of novel QTL for shoot and root traits in barley (Hordeum vulgare L.). Molecular Breeding, 34(3), 1373-1387.
Bishopp, A., & Lynch, J. P. (2015). The hidden half of crop yields. Nature Plants, 1(8), 1-2.
Burton, A. L., Johnson, J., Foerster, J., Hanlon, M. T., Kaeppler, S. M., Lynch, J. P., & Brown, K. M. (2015). QTL mapping and phenotypic variation of root anatomical traits in maize (Zea mays L.). Theoretical and Applied Genetics, 128(1), 93-106.
Chen, H. C., Song, J., Williams, C. M., Shuford, C. M., Liu, J., Wang, J. P.,... & Chiang, V.L. (2013). Monolignol pathway 4-coumaric acid: Coenzyme a ligases in populus. trichocarpa: Novel specificity, metabolic regulation, and simulation of coenzyme a ligation fluxes. Plant Physiology, 161(3), 1501-1516.
Cho, H. T., & Cosgrove, D. J. (2002). Regulation of root hair initiation and expansin gene expression in Arabidopsis. The Plant Cell, 14(12), 3237-3253.
Catolos, M., Sandhu, N., Dixit, S., Shamsudin, N. A., Naredo, M. E., McNally, K.L.,... & Kumar, A. (2017). Genetic loci governing grain yield and root development under variable rice cultivation conditions. Frontiers in Plant Science, 8, 1763.
Courtois, B., Shen, L., Petalcorin, W., Carandang, S., Mauleon, R., & Li, Z. (2003). Locating QTLs controlling constitutive root traits in the rice population IAC 165×Co39. Euphytica, 134(3), 335-345.
Courtois, B., Ahmadi, N., Khowaja, F., Price, A. H., Rami, J. F., Frouin, J.,... & Ruiz, M. (2009). Rice root genetic architecture: meta-analysis from a drought QTL database. Rice, 2(2), 115-128.
Darvasi, A., & Soller, M. (1997). A simple method to calculate resolving power and confidence interval of QTL map location. Behavior Genetics, 27(2), 125-132.
Daryani, P., Darzi Ramandi, H., Dezhsetan, S., Mirdar Mansuri, R., Hosseini Salekdeh, G., & Shobbar, Z. S. (2022). Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach. Theoretical and Applied Genetics, 135(1), 81-106.
Darzi-Ramandi, H., Shariati J, V., Tavakol, E., Najafi-Zarini, H., Bilgrami, S. S., & Razavi, K. (2017). Detection of consensus genomic regions associated with root architecture of bread wheat on groups 2 and 3 chromosomes using QTL meta-analysis. Australian Journal of Crop Science, 11(7), 777-785.
DeYoung, B. J., Bickle, K. L., Schrage, K. J., Muskett, P., Patel, K., & Clark, S. E. (2006). The CLAVATA1‐related BAM1, BAM2 and BAM3 receptor kinase‐like proteins are required for meristem function in Arabidopsis. The Plant Journal, 45(1), 1-16.
Ding, W., Yu, Z., Tong, Y., Huang, W., Chen, H., & Wu, P. (2009). A transcription factor with a bHLH domain regulates root hair development in rice. Cell research,19(11),1309-1311.
Ding, X., Li, X., & Xiong, L. (2011). Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theoretical and Applied Genetics, 123(5), 815-826.
Ellis, C.M., Nagpal, P., Young, J.C., Hagen, G., Guilfoyle, T.J., Reed, & J.W. (2005) Auxin response factor1 and auxin response factor2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development.,132, 4563-4574.
Emrich, K., Price, A., & Piepho, H.P. (2008) Assessing the importance of genotype×environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models. Euphytica. 161(1), 229-240.
Gamuyao, R., Chin, J. H., Pariasca-Tanaka, J., Pesaresi, P., Catausan, S., Dalid, C.,... & Heuer, S. (2012). The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature, 488(7412), 535-539.
Gierth, M., & Mäser, P. (2007). Potassium transporters in plants–involvement in K+ acquisition, redistribution and homeostasis. FEBS Letters, 581(12), 2348-2356.
Goffinet, B., & Gerber, S. (2000). Quantitative trait loci: a meta-analysis. Genetics, 155(1), 463-473.
Guo, B., Sleper, D. A., Lu, P., Shannon, J. G., Nguyen, H. T., & Arelli, P. R. (2006). QTLs Associated with Resistance to Soybean Cyst Nematode in Soybean Meta‐Analysis of QTL Locations-Retraction. Crop Science, 46(1), 202-202.
Guo, J., Chen, L., Li, Y., Shi, Y., Song, Y., Zhang, D.,... & Li, C. (2018). Meta-QTL analysis and identification of candidate genes related to root traits in maize. Euphytica, 214(12), 1-15.
Guseman, J. M., Webb, K., Srinivasan, C., & Dardick, C. (2017). DRO 1 influences root system architecture in Arabidopsis and Prunus species. The Plant Journal, 89(6), 1093-1105.
Horii, H., Nemoto, K., Miyamoto, N., & Harada, J. (2006). Quantitative trait loci for adventitious and lateral roots in rice. Plant Breeding, 125(2), 198-200.
Ikeda, H., Kamoshita, A., & Manabe, T. (2007). Genetic analysis of rooting ability of transplanted rice (Oryza sativa L.) under different water conditions. Journal of experimental botany, 58(2), 309-318.
Inukai, Y., Sakamoto, T., Ueguchi-Tanaka, M., Shibata, Y., Gomi, K., Umemura, I.,... & Matsuoka, M. (2005). Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling. The Plant Cell, 17(5), 1387-1396.
Jeong, J. S., Kim, Y. S., Redillas, M. C., Jang, G., Jung, H., Bang, S. W.,... & Kim, J.K. (2013). OsNAC5 overexpression enlarges root diameter in rice plants leading to enhanced drought tolerance and increased grain yield in the field. Plant Biotechnology Journal, 11(1), 101-114.
Kamoshita, A., Zhang, J., Siopongco, J. D. L. C., Sarkarung, S., Nguyen, H. T., & Wade, L. J. (2002). Effects of phenotyping environment on identification of quantitative trait loci for rice root morphology under anaerobic conditions. Crop Science, 42(1), 255-265.
Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S.,... & Matsumoto, T. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice, 6(1), 1-10.
Khowaja, F. S., Norton, G. J., Courtois, B., & Price, A. H. (2009). Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genomics, 10(1), 1-14.
Li, J., Zhu, S., Song, X., Shen, Y., Chen, H., Yu, J.,... & Deng, X. W. (2006). A rice glutamate receptor–like gene is critical for the division and survival of individual cells in the root apical meristem. The Plant Cell, 18(2), 340-349.
Li, H., Zhou, S. Y., Zhao, W. S., Su, S. C., & Peng, Y. L. (2009). A novel wall-associated receptor-like protein kinase gene, OsWAK1, plays important roles in rice blast disease resistance. Plant Molecular Biology, 69(3), 337-346.
Li, J., Wang, D., Xie, Y., Zhang, H., Hu, G., Li, J.,... & Li,Z. (2011). Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes. Journal of Genetics and Genomics, 38(11), 547-556.
Li, W. T., Liu, C., Liu, Y. X., Pu, Z. E., Dai, S. F., Wang, J. R.,... & Wei, Y. M. (2013). Meta-analysis of QTL associated with tolerance to abiotic stresses in barley. Euphytica, 189(1), 31-49.
Li, J., Han, Y., Liu, L., Chen, Y., Du, Y., Zhang, J.,... & Zhao, Q. (2015). qRT9, a quantitative trait locus controlling root thickness and root length in upland rice. Journal of Experimental Botany, 66(9), 2723-2732.
Li, X., Guo, Z., Lv, Y., Cen, X., Ding, X., Wu, H.,... & Xiong, L. (2017). Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study. PLoS Genetics, 13(7), e1006889.
Liang, Y. S., Zhan, X. D., Wang, H. M., Gao, Z. Q., chuan Lin, Z., Chen, D. B.,... & Cheng, S. H. (2013). Locating QTLs controlling several adult root traits in an elite Chinese hybrid rice. Gene, 526(2), 331-335.
Lobet, G., Draye, X., & Périlleux, C. (2013). An online database for plant image analysis software tools. Plant Methods, 9(1), 1-8.
Maccaferri, M., El-Feki, W., Nazemi, G., Salvi, S., Canè, M. A., Colalongo, M. C.,... & Tuberosa, R. (2016). Prioritizing quantitative trait loci for root system architecture in tetraploid wheat. Journal of Experimental Botany, 67(4), 1161-1178.
Manschadi, A. M., Hammer, G. L., Christopher, J. T., & Devoil, P. (2008). Genotypic variation in seedling root architectural traits and implications for drought adaptation in wheat (Triticum aestivum L.). Plant and soil, 303(1), 115-129.
Mirdar Mansuri, R., Shobbar, Z. S., Babaeian Jelodar, N., Ghaffari, M. R., Nematzadeh, G. A., & Asari, S. (2019). Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes. Rice, 12(1), 1-13.
Mao, S.L., Wei, Y. M., Cao, W., Lan, X. J., Yu, M., Chen, Z. M.,... & Zheng, Y. L. (2010). Confirmation of the relationship between plant height and Fusarium head blight resistance in wheat (Triticum aestivum L.) by QTL meta-analysis. Euphytica, 174(3), 343-356.
Marone, D., Russo, M. A., Laidò, G., De Vita, P., Papa, R., Blanco, A.,... & Mastrangelo, A. M. (2013). Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes. BMC Genomics, 14(1), 1-17.
McCouch, S. R., Teytelman, L., Xu, Y., Lobos, K. B., Clare, K., Walton, M.,... & Stein, L. (2002). Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research, 9(6), 199-207.
Niones, J. M., Inukai, Y., Suralta, R. R., & Yamauchi, A. (2015). QTL associated with lateral root plasticity in response to soil moisture fluctuation stress in rice. Plant and Soil, 391(1), 63-75.
Nguyen, T.T.T., Klueva, N., Chamareck, V., Aarti, A., Magpantay, G., Millena, A. C. M.,... & Nguyen, H. T. (2004). Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice. Molecular Genetics and Genomics, 272(1), 35-46.
Obara, M., Takeda, T., Hayakawa, T., & Yamaya, T. (2011). Mapping quantitative trait loci controlling root length in rice seedlings grown with low or sufficient supply using backcross recombinant lines derived from a cross between Oryza sativa L. and Oryza glaberrima Steud. Soil Science and Plant Nutrition, 57(1), 80-92.
Price, A. H., Steele, K. A., Moore, B. J., & Jones, R. G. W. (2002). Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes: II. Mapping quantitative trait loci for root morphology and distribution. Field Crops Research, 76(1), 25-43.
Prince, S. J., Song, L., Qiu, D., Maldonado dos Santos, J. V., Chai, C., Joshi, T.,... & Nguyen, H. T. (2015). Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genomics, 16(1), 1-20.
Zhao-ming, Q., Ya-nan, S., Qiong, W., Chun-yan, L., Guo-hua, H., & Qing-shan, C. (2011). A meta-analysis of seed protein concentration QTL in soybean. Canadian Journal of Plant Science, 91(1), 221-230.
Qu, Y., Mu, P., Zhang, H., Chen, C. Y., Gao, Y., Tian, Y.,... & Li, Z. (2008). Mapping QTLs of root morphological traits at different growth stages in rice. Genetica, 133(2), 187-200.
Sandhu, N., Torres, R. O., Sta Cruz, M. T., Maturan, P. C., Jain, R., Kumar, A., & Henry, A. (2015). Traits and QTLs for development of dry direct-seeded rainfed rice varieties. Journal of Experimental Botany, 66(1), 225-244.
Shao, H. B., Song, W. Y., & Chu, L. Y. (2008). Advances of calcium signals involved in plant anti-drought. Comptes Rendus Biologies, 331(8), 587-596.
Sharma, S., Xu, S., Ehdaie, B., Hoops, A., Close, T. J., Lukaszewski, A. J., & Waines, J. G. (2011). Dissection of QTL effects for root traits using a chromosome arm-specific mapping population in bread wheat. Theoretical and Applied Genetics, 122(4), 759-769.
Singh, S., Pradhan, S. K., Singh, A. K., & Singh, O.N. (2012). Marker validation in recombinant inbred lines and random varieties of rice for drought tolerance. Australian Journal of Crop Science, 6(4), 606.
Singhal, P., Jan, A. T., Azam, M., & Haq, Q. M. R. (2016). Plant abiotic stress: a prospective strategy of exploiting promoters as alternative to overcome the escalating burden. Frontiers in Life Science, 9(1), 52-63.
Srividya, A., Ramanarao, P. V., Sridhar, S., Jayaprada, M., Anuradha, G., Srilakshmi, B.,... & Vemireddy, L. R. (2011). Molecular mapping of QTLs for drought related traits at seedling stage under PEG induced stress conditions in rice. American Journal of Plant Sciences, 2(02), 190.
Shiu, S. H., & Bleecker, A. B. (2001). Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proceedings of the National Academy of Sciences, 98(19), 10763-10768.
Sosnowski, O., Charcosset, A., & Joets, J. (2012). BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms. Bioinformatics, 28(15), 2082-2083.
Steele, K. A., Virk, D. S., Kumar, R., Prasad, S. C., & Witcombe, J. R. (2007). Field evaluation of upland rice lines selected for QTLs controlling root traits. Field Crops Research, 101(2), 180-186.
Suji, K. K., Prince, K. S. J., Mankhar, P. S., Kanagaraj, P., Poornima, R., Amutha, K.,... & Babu, R. C. (2012). Evaluation of rice (Oryza sativa L.) near iso-genic lines with root QTLs for plant production and root traits in rainfed target populations of environment. Field Crops Research, 137, 89-96.
Swamy, B. P., Vikram, P., Dixit, S., Ahmed, H. U., & Kumar, A. (2011). Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics, 12(1), 1-18.
Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., & McCouch, S. (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research, 11(8), 1441-1452.
Uga, Y., Okuno, K., & Yano, M. (2010). Fine mapping of Sta1, a quantitative trait locus determining stele transversal area, on rice chromosome 9. Molecular Breeding, 26(3), 533-538.
Uga, Y., Okuno, K., & Yano, M. (2011). Dro1, a major QTL involved in deep rooting of rice under upland field conditions. Journal of Experimental Botany, 62(8), 2485-2494.
Uga, Y., Sugimoto, K., Ogawa, S., Rane, J., Ishitani, M., Hara, N.,... & Yano, M. (2013). Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nature Genetics, 45(9), 1097-1102.
Uga, Y., Kitomi, Y., Ishikawa, S., & Yano, M. (2015). Genetic improvement for root growth angle to enhance crop production. Breeding Science, 65(2), 111-119.
Van Ha, C., Le, D.T., Nishiyama, R., Watanabe, Y.A.S.U.K.O., Sulieman, S., Tran, U. T.,... & Tran, L. S. P. (2013). The auxin response factor transcription factor family in soybean: genome-wide identification and expression analyses during development and water stress. DNA Research, 20(5), 511-524.
Venuprasad, R., Shashidhar, H. E., Hittalmani, S., & Hemamalini, G. S. (2002). Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes. Euphytica, 128(3), 293-300.
Veyrieras, J. B., Goffinet, B., & Charcosset, A. (2007). MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinformatics, 8(1), 1-16.
Visscher, P. M., & Goddard, M. E. (2004). Prediction of the confidence interval of quantitative trait loci location. Behavior Genetics, 34(4), 477-482.
Wang, R., & Estelle, M. (2014). Diversity and specificity: auxin perception and signaling through the TIR1/AFB pathway. Current Opinion in Plant Biology, 21, 51-58.
Wang, Y., Xu, J., Deng, D., Ding, H., Bian, Y., Yin, Z.,... & Zhao, Y. (2016). A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.). Planta, 243(2), 459-471.
Wang, Y., Wang, D., Gan, T., Liu, L., Long, W., Wang, Y.,... & Wan, J. (2016). CRL6, a member of the CHD protein family, is required for crown root development in rice. Plant Physiology and Biochemistry, 105, 185-194.
Wissuwa, M., Yano, M., & Ae, N. (1998). Mapping of QTLs for phosphorus-deficiency tolerance in rice (Oryza sativa L.). Theoretical and Applied Genetics, 97(5), 777-783.
Woo, Y. M., Park, H. J., Su’udi, M., Yang, J. I., Park, J. J., Back, K.,... & An, G. (2007). Constitutively wilted 1, a member of the rice YUCCA gene family, is required for maintaining water homeostasis and an appropriate root to shoot ratio. Plant Molecular Biology, 65(1), 125-136.
Wu, W., & Cheng, S. (2014). Root genetic research, an opportunity and challenge to rice improvement. Field Crops Research, 165, 111-124.
Xu, C. G., Li, X. Q., Xue, Y., Huang, Y. W., Gao, J., & Xing, Y. Z. (2004). Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines. Theoretical and Applied Genetics, 109(3), 640-647.
Yamamoto, T., Yoshida, Y., Nakajima, K., Tominaga, M., Gyohda, A., Suzuki, H.,... & Koshiba, T. (2018). Expression of RSOsPR10 in rice roots is antagonistically regulated by jasmonate/ethylene and salicylic acid via the activator OsERF87 and the repressor OsWRKY76, respectively. Plant Direct, 2(3), e00049.
Yamauchi, T., Tanaka, A., Inahashi, H., Nishizawa, N. K., Tsutsumi, N., Inukai, Y., & Nakazono, M. (2019). Fine control of aerenchyma and lateral root development through AUX/IAA-and ARF-dependent auxin signaling. Proceedings of the National Academy of Sciences, 116(41), 20770-20775.
Yue, B., Xiong, L., Xue, W., Xing, Y., Luo, L., & Xu, C. (2005). Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil. Theoretical and Applied Genetics, 111(6), 1127-1136.
Zhang, S., Wang, S., Xu, Y., Yu, C., Shen, C., Qian, Q.,... & Qi, Y. (2015). The auxin response factor, OsARF 19, controls rice leaf angles through positively regulating OsGH 3‐5 and OsBRI 1. Plant, Cell & Environment, 38(4), 638-654.
Zhang, X., Shabala, S., Koutoulis, A., Shabala, L., & Zhou, M. (2017). Meta-analysis of major QTL for abiotic stress tolerance in barley and implications for barley breeding. Planta, 245(2), 283-295.
Zhao, L., Liu, H. J., Zhang, C. X., Wang, Q. Y., & Li, X. H. (2015). Meta-analysis of constitutive QTLs for disease resistance in maize and its synteny conservation in the rice genome. Genet. Mol. Res, 14, 961-970.
Zhou, Y., Dong, G., Tao, Y., Chen, C., Yang, B., Wu, Y.,... & Wang, Y. (2016). Mapping quantitative trait loci associated with toot traits using sequencing-based genotyping chromosome segment substitution lines derived from 9311 and Nipponbare in Rice (Oryza sativa L.). PLoS One, 11(3), e0151796.
Zheng, B. S., Ling, Y. A. N. G., Chuan-Zao, M. A. O., Zhang, W. P., & Ping, W. U. (2006). QTLs and candidate genes for rice root growth under flooding and upland conditions. Acta Genetica Sinica, 33(2), 141-151.
ZhiMing, Y., Bo, K., XiaoWei, H., ShaoLei, L., YouHuang, B., WoNa, D.,... & Ping, W. (2011). Root hair‐specific expansins modulate root hair elongation in rice. The Plant Journal, 66(5), 725-734.