Abstract
Maize (Zea mays L.) and Asian rice (Oryza sativa L.), two most important cereals for human nutrition, have undergone strong artificial selection during a long period of time. Currently, a number of genes with stronger signals of selection have been identified through combining genomic and population genetic approach, but research on artificial selection of maize and Asian rice is scarcely done from the perspective of phenotypic difference of a number of agronomic traits. In this study, such an investigation was carried out on the basis of 179 published studies about phenotypic quantitative trait locus (QTL) mapping of Zea and Oryza species via QTL sign test. At the overall level, the proportions of antagonistic QTLs of Zea and Oryza species were 0.2446 and 0.2382 respectively, deviating significantly from neutrality. It indicated that these two genera have undergone similar selection strength during their evolutionary process. A previous study showed that 4 traits undergoing the directional selection during domestication were identified in Asian rice via QTL sign test, and 16 individual traits in Asian rice and 38 ones in maize that newly detected in this study deviated significantly from neutrality as well, demonstrating the dominant influence of artificial selection on them. Moreover, analysis of different categories of cross type including O. sativa × Oryza rufipogon (perennial and annual forms) crosses, maize × teosinte (Zea mays subsp. parviglumis) crosses, O. sativa × O. sativa crosses, and maize × maize crosses showed that their proportions of antagonistic QTLs were 0.1869, 0.1467, 0.2649, and 0.2618 respectively. These results revealed that selection strength of domestication is significantly stronger than that of modern genetic improvement. However, interestingly, the proportion of antagonistic QTLs (0.1591) in maize × maize with long-term selection was very similar to that (0.1467) in the maize × teosinte (Zea mays subsp. parviglumis) crosses. It suggested that some favorable traits could be cultivated within a few decades if we carry out strong selection. In addition, the proportions of antagonistic QTLs of the widely cultivated hybrids of rice (Minghui 63 × Zhenshan 97) and maize (Zheng 58 × Chang 7-2) in China were 0.309 and 0.3472 respectively. It suggested that selection during modern genetic improvement has significantly acted on them.
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References
Anderson EC, Slatkin M (2003) Orr’s quantitative trait loci sign test under conditions of trait ascertainment. Genetics 165:445–446
Bommert P, Nagasawa NS, Jackson D (2013) Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet 45:334–337
Chen C, Ritland K (2013) Lineage-specific mapping of quantitative trait loci. Heredity 111:106–113
Doebley J (2004) The genetics of maize evolution. Annu Rev Genet 38:37–59
Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386:485–488
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321
Gao ZY, Zhao SC, He WM, Guo LB, Peng YL, Wang JJ, Guo XS, Zhang XM, Rao YC, Zhang C, Dong GJ, Zheng FY, Lu CX, Hu J, Zhou Q, Liu HJ, Wu HY, Xu J, Ni PX, Zeng DL, Liu DH, Tian P, Gong LH, Ye C, Zhang GH, Wang J, Tian FK, Xue DW, Liao Y, Zhu L, Chen MS, Li JY, Cheng SH, Zhang GY, Wang J, Qian Q (2013) Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. PNAS 110:14492–14497
Grillo MA, Li CB, Fowlkes AM, Briggeman TM, Zhou AL, Schemske DW, Sang T (2009) Genetic architecture for the adaptive origin of annual wild rice, Oryza nivara. Evolution 63:870–883
Guo JJ, Chen ZL, Liu ZP, Wang BB, Song WB, Li W, Chen J, Dai JR, Lai JS (2011) Identification of genetic factors affecting plant density response through QTL mapping of yield component traits in maize (Zea mays L.). Euphytica 182:409–422
House MA, Griswold CK, Lukens LN (2014) Evidence for selection on gene expression in cultivated rice (Oryza sativa). Mol Bio Evol 31:1514–1525
Hua JP, Xing YZ, Wu WR, Xu CG, Sun XL, Yu SB, Zhang QF (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. PNAS 100:2574–2579
Huang XH, Wei XH, Sang T, Zhao Q, Feng Q, Zhao Y, Li CY, Zhu CR, Lu TT, Zhang ZW, Li M, Fan DL, Guo YL, Wang AH, Wang L, Deng LW, Li WJ, Lu YQ, Weng QJ, Liu KY, Huang T, Zhou TY, Jing YF, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li JY, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–969
Huang XH, Zhao Y, Wei XH, Li CY, Wang AH, Zhao Q, Li WJ, Guo YL, Deng LW, Zhu CR, Fan DL, Lu YQ, Weng QJ, Liu KY, Zhou TY, Jing YF, Si LZ, Dong GJ, Huang T, Lu TT, Feng Q, Qian Q, Li JY, Han B (2012a) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–41
Huang XH, Kurata N, Wei XH, Wang ZX, Wang AH, Zhao Q, Zhao Y, Liu KY, Lu HY, Li WJ, Guo YL, Lu YQ, Zhou CC, Fan DL, Weng QJ, Zhu CR, Huang T, Zhang L, Wang YC, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan XP, Xu Q, Dong GJ, Zhan QL, Li CY, Fujiyama A, Toyoda A, Lu TT, Feng Q, Qian Q, Li JY, Han B (2012b) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–503
Hufford MB, Xu X, Heerwaarden JV, Pyhajarvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai JS, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang GY, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44:808–813
Hung HY, Shannon LM, Tian F, Bradbury PJ, Chen C, Flint-Garcia SA, McMullen MD, Ware D, Buckler ES, Doebley JF, Holland JB (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. PNAS 109:E1913–E1921
Ishii T, Numaguchi K, Miura K, Yoshida K, Thanh PT, Htun TM, Yamasaki M, Komeda N, Matsumoto T, Terauchi R, Ishikawa R, Ashikari M (2013) OsLG1 regulates a closed panicle trait in domesticated rice. Nat Genet 45:462–467
Jiao YP, Zhao HN, Ren LH, Song WB, Zeng B, Guo JJ, Wang BB, Liu ZP, Chen J, Li W, Zhang M, Xie SJ, Lai JS (2012) Genome-wide genetic changes during modern breeding of maize. Nat Genet 44:812–817
Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365–1369
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
Lai JS, Li RQ, Xu X, Jin WW, Xu ML, Zhao HN, Xiang ZK, Song WB, Ying K, Zhang M, Jiao YP, Ni PX, Zhang JG, Li D, Guo XS, Ye SJ, Li JS, Fu Y, Springer NM, Yang HM, Wang J, Dai JR, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1031
Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
Li CB, Zhou AL, Sang T (2006a) Rice domestication by reducing shattering. Science 311:1936–1939
Li CB, Zhou AL, Sang T (2006b) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170:185–194
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD (2011) Molecular evidence for a single evolutionary origin of domesticated rice. PNAS 108:8351–8356
Orr HA (1998) Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data. Genetics 149:2099–2104
Rieseberg LH, Widmer A, Arntz AM, Burke JM (2002) Directional selection is the primary cause of phenotypic diversification. PNAS 99:12242–12245
Sang T (2011) Toward the domestication of lignocellulosic energy crops: learning from food crop domestication. J Integr Plant Biol 53:96–104
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028
Tian F, Bradbury PJ, Brown PJ, Hung HY, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162
Wang DL, Zhu J, Li ZK, Paterson AH (1999a) Mapping QTLs with epistatic effects and QTL x environment interactions by mixed linear model approaches. Theor Appl Genet 99:1255–1264
Wang RL, Stec A, Hey J, Lukens L, Doebley J (1999b) The limits of selection during maize domestication. Nature 398:236–239
Westerbergh A, Doebley J (2002) Morphological traits defining species differences in wild relatives of maize are controlled by multiple quantitative trait loci. Evolution 56:273–283
Xie WB, Wang GW, Yuan M, Yao W, Lyn K, Zhao H, Yang M, Li PB, Zhang X, Yuan J, Wang QX, Liu F, Dong HX, Zhang LJ, Li XL, Meng XZ, Zhang W, Xiong LZ, He YQ, Wang SP, Yu SB, Xu CG, Luo J, Li XH, Xiao JH, Lian XM, Zhang QF (2015) Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection. PNAS 112:E5411–E5419
Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468
Zhou G, Chen Y, Yao W, Zhang CJ, Xie WB, Hua JP, Xing YZ, Xiao JH, Zhang QF (2012) Genetic composition of yield heterosis in an elite rice hybrid. PNAS 109:15847–15852
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Liu, H. Assessment of artificial selection in maize (Zea mays L.) and Asian rice (Oryza sativa L.) using QTL data. Genet Resour Crop Evol 64, 1561–1568 (2017). https://doi.org/10.1007/s10722-016-0454-4
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DOI: https://doi.org/10.1007/s10722-016-0454-4