Abou-Elwafa SF (2016) Association mapping for drought tolerance in barley at the reproductive stage. Cr Biol 339:51-59
Abou-Elwafa SF (2018) Identification of genes associated with drought tolerance in barley. Biologia Plantarum 62:299-306
Abou-Elwafa SF, Shehzad T (2018) Genetic identification and expression profiling of drought responsive genes in sorghum. Environmental and Experimental Botany 155:12-20
Ainsworth EA, Yendrek CR, Skoneczka JA, Long SP (2012) Accelerating yield potential in soybean: potential targets for biotechnological improvement. Plant, cell & environment 35:38-52
Basra AS (1995) Seed quality: basic mechanisms and agricultural implications
Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop science 48:1649-1664
Burris J, Edje O, Wahab A (1973) Effects of Seed Size on Seedling Performance in Soybeans: II. Seedling Growth and Photosynthesis and Field Performance 1. Crop Science 13:207-210
Cai H, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theoretical and Applied Genetics 104:1217-1228
Cailleux A (1945) Distinction des galets marins et fluviatiles. Bulletin de la Société géologique de France 5:375-404
Cao Y, Li S, Chen G, Wang Y, Bhat JA, Karikari B, Kong J, Gai J, Zhao T (2019) Deciphering the Genetic Architecture of Plant Height in Soybean Using Two RIL Populations Sharing a Common M8206 Parent. Plants 8:373
Cao Y, Li S, Wang Z, Chang F, Kong J, Gai J, Zhao T (2017) Identification of major quantitative trait loci for seed oil content in soybeans by combining linkage and genome-wide association mapping. Frontiers in plant science 8:1222
Cerdà A, Garcıa-Fayos P (2002) The influence of seed size and shape on their removal by water erosion. Catena 48:293-301
Cha-um S, Kirdmanee C (2011) Remediation of salt-affected soil by the addition of organic matter: an investigation into improving glutinous rice productivity. Scientia Agricola 68:406-410
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R (2020a) TBtools-an integrative toolkit developed for interactive analyses of big biological data. bioRxiv:289660
Chen J, Cao F, Li H, Shan S, Tao Z, Lei T, Liu Y, Xiao Z, Zou Y, Huang M, Abou-Elwafa SF (2020b) Genotypic variation in the grain photosynthetic contribution to grain filling in rice. Journal of Plant Physiology 253:153269
Cheng X, Wang S, Wang L, Wang S, Zong X, Wang P (2006) Descriptors and Data Standard for Adzuki Bean [Vigna angularis (Willd.) Ohwi & Ohashi]. China Agriculture Press, Beijing
Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971
Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC genomics 12:4
Cober E, Voldeng H, Frégeau‐Reid J (1997) Heritability of seed shape and seed size in soybean. Crop Science 37:1767-1769
Ebone LA, Caverzan A, Tagliari A, Chiomento JLT, Silveira DC, Chavarria G (2020) Soybean Seed Vigor: Uniformity and Growth as Key Factors to Improve Yield. Agronomy 10:545
Edwards Jr CJ, Hartwig EE (1971) Effect of seed size upon rate of germination in soybeans 1. Agronomy Journal 63:429-450
Fang C, Ma Y, Wu S, Liu Z, Wang Z, Yang R, Hu G, Zhou Z, Yu H, Zhang M (2017) Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome biology 18:1-14
Funatsuki H, Kawaguchi K, Matsuba S, Sato Y, Ishimoto M (2005) Mapping of QTL associated with chilling tolerance during reproductive growth in soybean. Theoretical and Applied Genetics 111:851-861
Galal A, Sharma S, Abou-Elwafa SF, Sharma S, Kopisch-Obuch F, Laubach E, Perovic D, Ordon F, Jung C (2014) Comparative QTL analysis of root lesion nematode resistance in barley. Theor Appl Genet 127:1399-1407
Hacisalihoglu G, Burton AL, Gustin JL, Eker S, Asikli S, Heybet EH, Ozturk L, Cakmak I, Yazici A, Burkey KO (2018) Quantitative trait loci associated with soybean seed weight and composition under different phosphorus levels. Journal of integrative plant biology 60:232-241
Hacisalihoglu G, Settles AM (2017) Quantification of seed ionome variation in 90 diverse soybean (Glycine max) lines. Journal of Plant Nutrition 40:2808-2817
Haig D (2013) Kin conflict in seed development: an interdependent but fractious collective. Annual review of cell and developmental biology 29:189-211
Han Y, Li D, Zhu D, Li H, Li X, Teng W, Li W (2012) QTL analysis of soybean seed weight across multi-genetic backgrounds and environments. Theoretical and Applied Genetics 125:671-683
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.). International Journal of Molecular Sciences 21:1040
Hoeck JA, Fehr WR, Shoemaker RC, Welke GA, Johnson SL, Cianzio SR (2003) Molecular marker analysis of seed size in soybean. Crop Science 43:68-74
Hu Z, Zhang H, Kan G, Ma D, Zhang D, Shi G, Hong D, Zhang G, Yu D (2013) Determination of the genetic architecture of seed size and shape via linkage and association analysis in soybean (Glycine max L. Merr.). Genetica 141:247-254
Hyten D, Pantalone V, Sams C, Saxton A, Landau-Ellis D, Stefaniak T, Schmidt M (2004) Seed quality QTL in a prominent soybean population. Theoretical and Applied Genetics 109:552-561
Jannink J-L, Moreau L, Charmet G, Charcosset A (2009) Overview of QTL detection in plants and tests for synergistic epistatic interactions. Genetica 136:225
Jeong N, Suh SJ, Kim M-H, Lee S, Moon J-K, Kim HS, Jeong S-C (2012) Ln is a key regulator of leaflet shape and number of seeds per pod in soybean. The Plant Cell 24:4807-4818
Jun TH, Freewalt K, Michel AP, Mian R (2014) Identification of novel QTL for leaf traits in soybean. Plant Breeding 133:61-66
Kajiya-Kanegae H, Takanashi H, Fujimoto M, Ishimori M, Ohnishi N, Fiona WW, Omollo EA, Kobayashi M, Yano K, Nakano M (2020) RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum Using a Japanese Landrace Takakibi NOG. Plant and Cell Physiology
Karikari B, Li S, Bhat JA, Cao Y, Kong J, Yang J, Gai J, Zhao T (2019) Genome-wide detection of major and epistatic effect QTLs for seed protein and oil content in soybean under multiple environments using high-density bin map. International journal of molecular sciences 20:979
Kato S, Sayama T, Fujii K, Yumoto S, Kono Y, Hwang T-Y, Kikuchi A, Takada Y, Tanaka Y, Shiraiwa T (2014) A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds. Theoretical and Applied Genetics 127:1365-1374
Kaushik N, Kumar K, Kumar S, Kaushik N, Roy S (2007) Genetic variability and divergence studies in seed traits and oil content of Jatropha (Jatropha curcas L.) accessions. Biomass and Bioenergy 31:497-502
Khan NA, Githiri SM, Benitez ER, Abe J, Kawasaki S, Hayashi T, Takahashi R (2008) QTL analysis of cleistogamy in soybean. Theoretical and Applied Genetics 117:479-487
Kundu A, Chakraborty A, Mandal NA, Das D, Karmakar PG, Singh NK, Sarkar D (2015) A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae sl). Molecular Breeding 35:19
Li D, Sun M, Han Y, Teng W, Li W (2010) Identification of QTL underlying soluble pigment content in soybean stems related to resistance to soybean white mold (Sclerotinia sclerotiorum). Euphytica 172:49-57
Li N, Li Y (2014) Ubiquitin-mediated control of seed size in plants. Frontiers in plant science 5:332
Li S, Cao Y, He J, Zhao T, Gai J (2017) Detecting the QTL-allele system conferring flowering date in a nested association mapping population of soybean using a novel procedure. Theoretical and Applied Genetics 130:2297-2314
Li W, Zheng D-H, Van K, Lee S-H (2008) QTL mapping for major agronomic traits across two years in soybean (Glycine max L. Merr.). J Crop Sci Biotechnol 11:171-190
Liang H, Xu L, Yu Y, Yang H, Dong W, Zhang H (2016) Identification of QTLs with main, epistatic and QTL by environment interaction effects for seed shape and hundred-seed weight in soybean across multiple years. Journal of genetics 95:475-477
Liu D, Yan Y, Fujita Y, Xu D (2018) Identification and validation of QTLs for 100-seed weight using chromosome segment substitution lines in soybean. Breeding science 68:442-448
Liu N, Li M, Hu X, Ma Q, Mu Y, Tan Z, Xia Q, Zhang G, Nian H (2017) Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing. BMC genomics 18:466
Lu X, Xiong Q, Cheng T, Li Q-T, Liu X-L, Bi Y-D, Li W, Zhang W-K, Ma B, Lai Y-C (2017) A PP2C-1 allele underlying a quantitative trait locus enhances soybean 100-seed weight. Molecular Plant 10:670-684
Ma J, Wingen LU, Orford S, Fenwick P, Wang J, Griffiths S (2015) Using the UK reference population Avalon× Cadenza as a platform to compare breeding strategies in elite Western European bread wheat. Molecular Breeding 35:70
Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proceedings of the National Academy of Sciences 107:19579-19584
Meng Y, Chen F, Shuai H, Luo X, Ding J, Tang S, Xu S, Liu J, Liu W, Du J (2016) Karrikins delay soybean seed germination by mediating abscisic acid and gibberellin biogenesis under shaded conditions. Scientific reports 6:1-12
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome research 17:240-248
Mohan M, Nair S, Bhagwat A, Krishna T, Yano M, Bhatia C, Sasaki T (1997) Genome mapping, molecular markers and marker-assisted selection in crop plants. Molecular breeding 3:87-103
Moongkanna J, Nakasathien S, Novitzky W, Kwanyuen P, Sinchaisri P, Srinives P (2011) SSR markers linking to seed traits and total oil content in soybean. Thai Journal of Agricultural Science 44:233-241
Morton NE (1955) Sequential tests for the detection of linkage. American journal of human genetics 7:277
Nyquist WE, Baker R (1991) Estimation of heritability and prediction of selection response in plant populations. Critical reviews in plant sciences 10:235-322
Omokhafe K, Alika J (2004) Clonal variation and correlation of seed characters in Hevea brasiliensis Muell. Arg. Industrial Crops and Products 19:175-184
Palomeque L, Li-Jun L, Li W, Hedges B, Cober ER, Rajcan I (2009) QTL in mega-environments: II. Agronomic trait QTL co-localized with seed yield QTL detected in a population derived from a cross of high-yielding adapted× high-yielding exotic soybean lines. Theoretical and Applied Genetics 119:429-436
Palomeque L, Liu L-J, Li W, Hedges BR, Cober ER, Smid MP, Lukens L, Rajcan I (2010) Validation of mega-environment universal and specific QTL associated with seed yield and agronomic traits in soybeans. Theoretical and applied genetics 120:997-1003
Pan L, Wang N, Wu Z, Guo R, Yu X, Zheng Y, Xia Q, Gui S, Chen C (2017) A high density genetic map derived from RAD sequencing and its application in QTL analysis of yield-related traits in Vigna unguiculata. Frontiers in plant science 8:1544
Panthee D, Pantalone V, West D, Saxton A, Sams C (2005) Quantitative trait loci for seed protein and oil concentration, and seed size in soybean. Crop Science 45:2015-2022
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS one 7:e37135
Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PloS one 7:e32253
Qi Z-m, Wu Q, Han X, Sun Y-n, Du X-y, Liu C-y, Jiang H-w, Hu G-h, Chen Q-s (2011) Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes. Euphytica 179:499-514
Salas P, Oyarzo-Llaipen J, Wang D, Chase K, Mansur L (2006) Genetic mapping of seed shape in three populations of recombinant inbred lines of soybean (Glycine max L. Merr.). Theoretical and Applied Genetics 113:1459-1466
Severin AJ, Woody JL, Bolon Y-T, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE (2010) RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC plant biology 10:160
Smith T, Camper Jr H (1975) Effects of seed size on soybean performance. Agronomy Journal 67:681-684
Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PloS one 8:e58700
Sun Y-n, Pan J-b, Shi X-l, Du X-y, Wu Q, Qi Z-m, Jiang H-w, Xin D-w, Liu C-y, Hu G-h (2012) Multi-environment mapping and meta-analysis of 100-seed weight in soybean. Molecular Biology Reports 39:9435-9443
Tao Y, Mace ES, Tai S, Cruickshank A, Campbell BC, Zhao X, Van Oosterom EJ, Godwin ID, Botella JR, Jordan DR (2017) Whole-genome analysis of candidate genes associated with seed size and weight in sorghum bicolor reveals signatures of artificial selection and insights into parallel domestication in cereal crops. Frontiers in plant science 8:1237
Tasma I, Lorenzen L, Green D, Shoemaker R (2001) Mapping genetic loci for flowering time, maturity, and photoperiod insensitivity in soybean. Molecular Breeding 8:25-35
Teng W, Feng L, Li W, Wu D, Zhao X, Han Y, Li W (2017) Dissection of the genetic architecture for soybean seed weight across multiple environments. Crop and Pasture Science 68:358-365
Teng W, Han Y, Du Y, Sun D, Zhang Z, Qiu L, Sun G, Li W (2009) QTL analyses of seed weight during the development of soybean (Glycine max L. Merr.). Heredity 102:372-380
Tewodros M, Zelalem B (2016) Advances in Quantitative Trait Loci, mapping and importance of Markers Assisted Selection in plant breeding research. International Journal of Plant Breeding and Genetics 10:58-68
Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, Xu W, Su Z (2017) agriGO v2. 0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic acids research 45:W122-W129
Tomooka N, Vaughan D, Maxted N, Moss H (2002) The Asian Vigna: genus Vigna subgenus ceratotropis genetic resources. Springer Science & Business Media
Vieira AJD, Oliveira DAd, Soares TCB, Schuster I, Piovesan ND, Martínez CA, Barros EGd, Moreira MA (2006) Use of the QTL approach to the study of soybean trait relationships in two populations of recombinant inbred lines at the F7 and F8 generations. Brazilian Journal of Plant Physiology 18:281-290
Wang C, Rutledge J, Gianola D (1994) Bayesian analysis of mixed linear models via Gibbs sampling with an application to litter size in Iberian pigs. Genetics Selection Evolution 26:91-115
Wang D, Bales-Arcelo C, Zhang Z, Gu C, DiFonzo CD, Zhang G, Yang Z, Liu M, Mensah C (2019) Sources of aphid resistance in soybean plants. Google Patents
Wang S, Basten C, Zeng Z (2006) Windows QTL Cartographer 2.5. Dep. of Statistics, North Carolina State Univ., Raleigh. Windows QTL cartographer 25 Dep of Statistics, North Carolina State Univ, Raleigh:-
Wu D, Zhan Y, Sun Q, Xu L, Lian M, Zhao X, Han Y, Li W (2018) Identification of quantitative trait loci underlying soybean (Glycine max [L.] Merr.) seed weight including main, epistatic and QTL× environment effects in different regions of Northeast China. Plant Breeding 137:194-202
Wu Y, Gong W, Yang W (2017) Shade inhibits leaf size by controlling cell proliferation and enlargement in soybean. Scientific reports 7:1-10
Xie F-T, Niu Y, Zhang J, Bu S-H, Zhang H-Z, Geng Q-C, Feng J-Y, Zhang Y-M (2014) Fine mapping of quantitative trait loci for seed size traits in soybean. Molecular Breeding 34:2165-2178
Xie M, Ming Y, Shao F, Jian J, Zhang Y, Peng Z (2018) Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (Silurus meridionalis). Royal Society open science 5:172054
Xin D, Qi Z, Jiang H, Hu Z, Zhu R, Hu J, Han H, Hu G, Liu C, Chen Q (2016) QTL location and epistatic effect analysis of 100-seed weight using wild soybean (Glycine soja Sieb. & Zucc.) chromosome segment substitution lines. PloS one 11:e0149380
Xing G, Zhou B, Wang Y, Zhao T, Yu D, Chen S, Gai J (2012) Genetic components and major QTL confer resistance to bean pyralid (Lamprosema indicata Fabricius) under multiple environments in four RIL populations of soybean. Theoretical and Applied Genetics 125:859-875
Xu Y, Li H-N, Li G-J, Wang X, Cheng L-G, Zhang Y-M (2011) Mapping quantitative trait loci for seed size traits in soybean (Glycine max L. Merr.). Theoretical and Applied Genetics 122:581-594
Yamanaka N, Ninomiya S, Hoshi M, Tsubokura Y, Yano M, Nagamura Y, Sasaki T, Harada K (2001) An informative linkage map of soybean reveals QTLs for flowering time, leaflet morphology and regions of segregation distortion. DNA research 8:61-72
Yang BZ, Zhao H, Kranzler HR, Gelernter J (2005) Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE. Genetic Epidemiology: The Official Publication of the International Genetic Epidemiology Society 28:302-312
Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24:721-723
Yang J, Zhu J, Williams RW (2007) Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 23:1527-1536
Yang K, Moon J-K, Jeong N, Chun H-K, Kang S-T, Back K, Jeong S-C (2011) Novel major quantitative trait loci regulating the content of isoflavone in soybean seeds. Genes & Genomics 33:685-692
Yao D, Wang P, Zhang J, Liu Z, Guan S, Liu S, Qu J (2014) A QTL mapping analysis of main yield traits in soybean. Journal of South China Agricultural University 35:41-46
Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L (2006) WEGO: a web tool for plotting GO annotations. Nucleic acids research 34:W293-W297
Zeng Z-B (1994) Precision mapping of quantitative trait loci. Genetics 136:1457-1468
Zhang F, Kang J, Long R, Yu L-X, Wang Z, Zhao Z, Zhang T, Yang Q (2019a) High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq. BMC plant biology 19:165
Zhang H, Chen J, Shan S, Cao F, Chen G, Zou Y, Huang M, Abou-Elwafa SF (2020) Proteomic profiling reveals differentially expressed proteins associated with amylose accumulation during rice grain filling. BMC Genomics 21:714
Zhang W-K, Wang Y-J, Luo G-Z, Zhang J-S, He C-Y, Wu X-L, Gai J-Y, Chen S-Y (2004) QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theoretical and Applied Genetics 108:1131-1139
Zhang X, Hina A, Song S, Kong J, Bhat JA, Zhao T (2019b) Whole-genome mapping identified novel “QTL hotspots regions” for seed storability in soybean (Glycine max L.). BMC genomics 20:499
Zhang Y, Li W, Lin Y, Zhang L, Wang C, Xu R (2018) Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing. BMC genomics 19:641
Zhao B, Dai A, Wei H, Yang S, Wang B, Jiang N, Feng X (2016) ArabidopsisKLU homologue GmCYP78A72 regulates seed size in soybean. Plant molecular biology 90:33-47
Zhao F, Xu S (2012) Genotype by environment interaction of quantitative traits: a case study in barley. G3: Genes, Genomes, Genetics 2:779-788
Zhaoming Q, Xiaoying Z, Huidong Q, Dawei X, Xue H, Hongwei J, Zhengong Y, Zhanguo Z, Jinzhu Z, Rongsheng Z (2017) Identification and validation of major QTLs and epistatic interactions for seed oil content in soybeans under multiple environments based on a high-density map. Euphytica 213:162