Almeida-Silva F, Pedrosa-Silva F, Venancio T M. 2023. The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples. The Plant Journal, 116, 1041–1051.
Anderson E J, Ali M L, Beavis W D, Chen P Y, Clemente T E, Diers B W, Graef G L, Grassini P, Hyten D L, McHale L K, Nelson R L, Parrott W A, Patil G B, Stupar R M, Tilmon K J. 2019. Soybean [Glycine max (L.) Merr.] breeding: History, improvement, production and future opportunities. In: Al-Khayri J M, Jain S M, Johnson D V, ed., Advances in Plant Breeding Strategies: Legumes. Springer Publishing, Cham, Switzerland. pp. 431–516.
Angkawijaya A E, Nguyen V C, Nakamura Y. 2017. Enhanced root growth in phosphate-starved Arabidopsis by stimulating de novo phospholipid biosynthesis through the overexpression of LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE 2 (LPAT2). Plant Cell and Environment, 40, 1807–1818.
Angkawijaya A E, Nguyen V C, Nakamura Y. 2019. LYSOPHOSPHATIDIC ACID ACYLTRANSFERASES 4 and 5 are involved in glycerolipid metabolism and nitrogen starvation response in Arabidopsis. New Phytologist, 224, 336–351.
Boyes D C, Zayed A M, Ascenzi R, McCaskill A J, Hoffman N E, Davis K R, Görlach J. 2001. Growth stage–based phenotypic analysis of Arabidopsis: A model for high throughput functional genomics in plants. The Plant Cell, 13, 1499–1510.
Brensha W, Kantartzi S K, Meksem K, Grier R L, Barakat A, Lightfoot D A, Kassem M A. 2012. Genetic analysis of root and shoot traits in the ‘Essex’ by ‘Forrest’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.]. Journal of Plant Genome Sciences, 1, 1–9.
Cadzow M, Boocock J, Nguyen H T, Wilcox P, Merriman T R, Black M A. 2014. A bioinformatics workflow for detecting signatures of selection in genomic data. Frontiers in Genetics, 5, 293.
Cao S H, Luo X M, Xu D G, Tian X L, Song J, Xia X C, Chu C C, He Z H. 2021. Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals. New Phytologist, 230, 1731–1745.
Chen G Q, van Erp H, Martin-Moreno J, Johnson K, Morales E, Browse J, Eastmond P J, Lin J T. 2016. Expression of castor LPAT2 enhances ricinoleic acid content at the sn-2 position of triacylglycerols in lesquerella seed. International Journal of Molecular Sciences, 17, 507.
Chen H T, Kumawat G, Yan Y L, Fan B J, Xu D H. 2021. Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions. BMC Genomics, 22, 132.
Chen S L, Lei Y, Xu X, Huang J Q, Jiang H F, Wang J, Cheng Z S, Zhang J N, Song Y H, Liao B S, Li Y R. 2015. The peanut (Arachis hypogaea L.) gene AhLPAT2 increases the lipid content of transgenic Arabidopsis seeds. PLoS ONE, 10, e0136170.
Clough S J, Bent A F. 1998. Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. The Plant Journal, 16, 735–743.
Cronk B C. 2017. How to Use IBM SPSS Statistics: A Step-by-Step Guide to Analysis and Interpretation, Eighth Edi. Routledge Publishing, New York, USA.
Dong S S, He W M, Ji J J, Zhang C, Guo Y, Yang T L. 2021. LDBlockShow: A fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. Briefings in Bioinformatics, 22, bbaa227.
Fageria N K, Moreira A. 2011. The role of mineral nutrition on root growth of crop plants. In: Sparks D L, ed., Advances in Agronomy. Academic Press Publishing, New York, USA. pp. 251–331.
van Gelderen K, Kang C K, Pierik R. 2018. Light signaling, root development, and plasticity. Plant Physiology, 176, 1049–1060.
Guseman J M, Webb K, Srinivasan C, Dardick C. 2017. DRO1 influences root system architecture in Arabidopsis and Prunus species. The Plant Journal, 89, 1093–1105.
Hao Y J, Wei W, Song Q X, Chen H W, Zhang Y Q, Wang F, Zou H F, Lei G, Tian A G, Zhang W K, Ma B, Zhang J S, Chen S Y. 2011. Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants. The Plant Journal, 68, 302–313.
Hassidim M, Harir Y, Yakir E, Kron I, Green R M. 2009. Over-expression of CONSTANS-LIKE 5 can induce flowering in short-day grown Arabidopsis. Planta, 230, 481–491.
Hu D D, Cui R F, Wang K, Yang Y M, Wang R Y, Zhu H Q, He M S, Fan Y K, Wang L, Wang L, Chu S S, Zhang J Y, Zhang S S, Yang Y F, Zhai X H, Lü H Y, Zhang D D, Wang J S, Kong F J, Yu D Y, et al. 2024. The Myb73-GDPD2-GA2ox1 transcriptional regulatory module confers phosphate deficiency tolerance in soybean. The Plant Cell, 36, 2176–2200.
Hu Y, Liu Y, Tao J J, Lu L, Jiang Z H, Wei J J, Wu C M, Yin C C, Li W, Bi Y D, Lai Y C, Wei W, Zhang W K, Chen S Y, Zhang J S. 2023. GmJAZ3 interacts with GmRR18a and GmMYC2a to regulate seed traits in soybean. Journal of Integrative Plant Biology, 65, 1983–2000.
Huang P H, Lu M Y, Li X B, Sun H Y, Cheng Z Y, Miao Y C, Fu Y F, Zhang X M. 2022. An efficient Agrobacterium rhizogenes-mediated hairy root transformation method in a soybean root biology study. International Journal of Molecular Sciences, 23, 12261.
Hyten D L. 2022. Genotyping platforms for genome-wide association studies: Options and practical considerations. In: Torkamaneh D, Belzile F, eds., Genome-Wide Association Studies. Humana Publishing, New York, USA. pp. 29–42.
Kim H U, Huang A H C. 2004. Plastid lysophosphatidyl acyltransferase is essential for embryo development in Arabidopsis. Plant Physiology, 134, 1206–1216.
Kim H U, Li Y B, Huang A H C. 2005. Ubiquitous and endoplasmic reticulum-located lysophosphatidyl acyltransferase, LPAT2, is essential for female but not male gametophyte development in Arabidopsis. The Plant Cell, 17, 1073-89.
Kim H U, Vijayan P, Carlsson A S, Barkan L, Browse J. 2010. A mutation in the LPAT1 gene suppresses the sensitivity of fab1 plants to low temperature. Plant Physiology, 153, 1135–1143.
Kim S H, Tayade R, Kang B H, Hahn B S, Ha B K, Kim Y H. 2023. Genome-wide association studies of seven root traits in soybean (Glycine max L.) landraces. International Journal of Molecular Sciences, 24, 873.
Körbes A P, Kulcheski F R, Margis R, Margis-Pinheiro M, Turchetto-Zolet A C. 2016. Molecular evolution of the lysophosphatidic acid acyltransferase (LPAAT) gene family. Molecular Phylogenetics and Evolution, 96, 55–69.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547–1549.
Li X, Hu D Z, Cai L Y, Wang H Q, Liu X Y, Du H P, Yang Z Y, Zhang H R, Hu Z B, Huang F, Kan G Z, Kong F J, Liu B H, Yu D Y, Wang H. 2022. CALCIUM-DEPENDENT PROTEIN KINASE38 regulates flowering time and common cutworm resistance in soybean. Plant Physiology, 190, 480–499.
Li Y, Gu J B, Zhao B Y, Yuan J B, Li C, Lin Y, Chen Y H, Yang X L, Li Y, Wang Z Y. 2024. Identification and confirmation of novel genetic loci and domestication gene GmGA20ox1 regulating primary root length in soybean seedling stage. Industrial Crops and Products, 217, 118814.
Liang H Z, Yu Y L, Yang H Q, Xu L J, Dong W, Du H, Cui W W, Zhang H Y. 2014. Inheritance and QTL mapping of related root traits in soybean at the seedling stage. Theoretical and Applied Genetics, 127, 2127–2137.
Liu X Q, Yang Y M, Wang R Y, Cui R F, Xu H Q, Sun C Y, Wang J S, Zhang H Y, Chen H T, Zhang D. 2022. GmWRKY46, a WRKY transcription factor, negatively regulates phosphorus tolerance primarily through modifying root morphology in soybean. Plant Science, 315, 111148.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods, 25, 402–408.
Lu S J, Dong L D, Fang C, Liu S L, Kong L P, Cheng Q, Chen L Y, Su T, Nan H Y, Zhang D, Zhang L, Wang Z J, Yang Y Q, Yu D Y, Liu X L, Yang Q Y, Lin X Y, Tang Y, Zhao X H, Yang X Q, et al. 2020. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nature Genetics, 52, 428–436.
Mandozai A, Moussa A A, Zhang Q, Qu J, Du Y Y, Anwari G, Amin N A, Wang P W. 2021. Genome-wide association study of root and shoot related traits in spring soybean (Glycine max L.) at seedling stages using SLAF-Seq. Frontiers in Plant Science, 12, 568995.
Marsh J. 2022. Linkage disequilibrium statistics and block visualization. In: Edwards D, ed., Plant Bioinformatics: Methods and Protocols. Humana Publishing, New York, USA. pp. 483–496.
Misra N, Panda P K, Parida B K. 2014. Genome-wide identification and evolutionary analysis of algal LPAT genes involved in TAG biosynthesis using bioinformatic approaches. Molecular Biology Reports, 41, 8319–8332.
van Nguyen L, Takahashi R, Githiri S M, Rodriguez T O, Tsutsumi N, Kajihara S, Sayama T, Ishimoto M, Harada K, Suematsu K, Abiko T, Mochizuki T. 2017. Mapping quantitative trait loci for root development under hypoxia conditions in soybean (Glycine max L. Merr.). Theoretical and Applied Genetics, 130, 743–755.
Noh E, Fallen B, Payero J, Narayanan S. 2022. Parsimonious root systems and better root distribution can improve biomass production and yield of soybean. PLoS ONE, 17, e0270109.
O’Malley R C, Barragan C C, Ecker J R. 2015. A user’s guide to the Arabidopsis T-DNA insertion mutant collections. In: lonso J, Stepanova A, eds., Plant Functional Genomics: Methods and Protocols. Humana Publishing, New York, USA. pp. 323–342.
Prince S J, Vuong T D, Wu X L, Bai Y H, Lu F, Kumpatla S P, Valliyodan B, Shannon J G, Nguyen H T. 2020. Mapping quantitative trait loci for soybean seedling shoot and root architecture traits in an inter-specific genetic population. Frontiers in Plant Science, 11, 1284.
Shaikh A A, Alamin A, Jia C X, Gong W, Deng X J, Shen Q W, Hong Y Y. 2022. The examination of the role of rice lysophosphatidic acid acyltransferase 2 in response to salt and drought stresses. International Journal of Molecular Sciences, 23, 9796.
Sun M L, Li Y, Zheng J Q, Wu D P, Li C X, Li Z Y, Zang Z W, Zhang Y Z, Fang Q W, Li W B, Han Y P, Zhao X, Li Y G. 2022. A nuclear factor Y-B transcription factor, GmNFYB17, regulates resistance to drought stress in soybean. International Journal of Molecular Sciences, 23, 7242.
Turner S D. 2018. qqman: An R package for visualizing GWAS results using Q-Q and manhattan plots. The Journal of Open Source Software, 3, 731.
Wang J B, Zhang Z W. 2021. GAPIT version 3: Boosting power and accuracy for genomic association and prediction. Genomics Proteomics Bioinformatics, 19, 629–640.
Wang X, Zhou S D, Wang J, Lin W X, Yao X L, Su J Q, Li H Y, Fang C, Kong F J, Guan Y F. 2023. Genome-wide association study for biomass accumulation traits in soybean. Molecular Breeding, 43, 33.
Wang Z L, Huang C, Niu Y C, Yung W S, Xiao Z X, Wong F L, Huang M K, Wang X, Man C K, Sze C C, Liu A L, Wang Q W, Chen Y L, Liu S, Wu C X, Liu L F, Hou W S, Han T F, Li M W, Lam H M. 2022. QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits. Theoretical and Applied Genetics, 135, 4507–4522.
Wattelet-Boyer V, Guédard M L, DIttrich-Domergue F, Maneta-Peyret L, Kriechbaumer V, Boutté Y, Bessoule J J, Moreau P. 2022. Lysophosphatidic acid acyltransferases: A link with intracellular protein trafficking in Arabidopsis root cells? Journal of Experimental Botany, 73, 1327–1343.
Wayne L L, Gachotte D J, Graupner P R, Adelfinskaya Y, McCaskill D G, Metz J G, Zirkle R, Walsh T A. 2021. Plant and algal lysophosphatidic acid acyltransferases increase docosahexaenoic acid accumulation at the sn-2 position of triacylglycerol in transgenic Arabidopsis seed oil. PLoS ONE, 16, e0256625.
Wen X X, Zhong Z Z, Xu P, Yang Q Q, Wang Y P, Liu L, Wu Z Z, Wu Y W, Zhang Y X, Liu Q N, Zhou Z P, Peng Z Q, He Y Q, Cheng S H, Cao L Y, Zhan X D, Wu W X. 2024. OsCOL5 suppresses heading through modulation of Ghd7 and Ehd2, enhancing rice yield. Theoretical and Applied Genetics, 137, 162.
Yang H, Shi G X, Du H Y, Wang H, Zhang Z Z, Hu D Z, Wang J, Huang F, Yu D Y. 2017. Genome-wide analysis of soybean LATERAL ORGAN BOUNDARIES Domain‐containing genes: A functional investigation of GmLBD12. The Plant Genome, 10, 1–19.
Yang X F, Kim M Y, Ha J M, Lee S H. 2019. Overexpression of the soybean NAC gene GmNAC109 increases lateral root formation and abiotic stress tolerance in transgenic Arabidopsis plants. Frontiers in Plant Science, 10, 1036.
Yang Y M, Wang L, Zhang D, Che Z J, Wang Q, Cui R F, Zhao W, Huang F, Zhang H Y, Cheng H, Yu D Y. 2024. Soybean type-B response regulator GmRR1 mediates phosphorus uptake and yield by modifying root architecture. Plant Physiology, 194, 1527–1544.
Yang Z Q, Luo C F, Pei X X, Wang S B, Huang Y M, Li J W, Liu B H, Kong F J, Yang Q Y, Fang C. 2024. SoyMD: A platform combining multi-omics data with various tools for soybean research and breeding. Nucleic Acids Research, 52, D1639–D1650.
Ye H, Song L, Chen H T, Valliyodan B, Cheng P, Ali L, Vuong T, Wu C J, Orlowski J, Buckley B, Chen P Y, Shannon J G, Nguyen H T. 2018. A major natural genetic variation associated with root system architecture and plasticity improves waterlogging tolerance and yield in soybean. Plant Cell and Environment, 41, 2169–2182.
Yin L L, Zhang H H, Tang Z S, Xu J Y, Yin D, Zhang Z W, Yuan X H, Zhu M J, Zhao S H, Li X Y, Liu X L. 2021. rMVP: A memory-efficient, visualization-enhanced, and parallel-accelerated tool for genome-wide association study. Genomics Proteomics Bioinformatics, 19, 619–628.
Yin Y T, Raboanatahiry N, Chen K, Chen X F, Tian T, Jia J, He H S, He J J, Guo Z Y, Yu L J, Li M T. 2022. Class A lysophosphatidic acid acyltransferase 2 from Camelina sativa promotes very long-chain fatty acids accumulation in phospholipid and triacylglycerol. The Plant Journal, 112, 1141–1158.
Yu B, Wakao S, Fan J L, Benning C. 2004. Loss of plastidic lysophosphatidic acid acyltransferase causes embryo-lethality in Arabidopsis. Plant and Cell Physiology, 45, 503–510.
Zhang C, Dong S S, Xu J Y, He W M, Yang T L. 2019. PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35, 1786–1788.
Zhang K, He J J, Yin Y T, Chen K, Deng X, Yu P, Li H X, Zhao W G, Yan S X, Li M T. 2022. Lysophosphatidic acid acyltransferase 2 and 5 commonly, but differently, promote seed oil accumulation in Brassica napus. Biotechnology for Biofuels and Bioproducts, 15, 83.
Zhang W X, Zhi W J, Qiao H, Huang J J, Li S, Lu Q, Wang N, Li Q, Zhou Q, Sun J Q, Bai Y T, Zheng X J, Bai M Y, Breusegem F V, Xiang F N. 2024. H2O2-dependent oxidation of the transcription factor GmNTL1 promotes salt tolerance in soybean. The Plant Cell, 36, 112–135.
Zhang X Y, Jia H Y, Li T, Wu J Z, Nagarajan R, Lei L, Powers C, Kan C C, Hua W, Liu Z Y, Chen C, Carver B F, Yan L L. 2022. TaCol-B5 modifies spike architecture and enhances grain yield in wheat. Plant Science, 376, 180–183.
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