Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (4): 579-590.doi: 10.3864/j.issn.0578-1752.2019.04.001
• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Next Articles
[1] |
PIPERNO D R, RANERE A J, HOLST I, IRIARTE J, DICKAU R . Starch grain and phytolith evidence for early ninth millennium BP maize from the Central Balsas River Valley, Mexico. Proceedings of the National Academy of Sciences of the United States of America, 2009,106(13):5019-5024.
doi: 10.1073/pnas.0812525106 pmid: 19307570 |
[2] |
MATSUOKA Y, VIGOUROUX Y, GOODMAN M M, SANCHEZ J, BUCKLER E, DOEBLEY J . A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of the United States of America, 2002,99(9):6080-6084.
doi: 10.1073/pnas.052125199 pmid: 11983901 |
[3] |
VAN HEERWAARDEN J, DOEBLEY J, BRIGGS W H, GLAUBITZ J C, GOODMAN M M, GONZALEZ J D J S, ROSS-IBARRA J . Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proceedings of the National Academy of Sciences of the United States of America, 2011,108(3):1088-1092.
doi: 10.1073/pnas.1013011108 pmid: 21189301 |
[4] |
BUCKLER E S, HOLLAND J B, BRADBURY P J, ACHARYA C B, BROWN P J, BROWNE C, ERSOZ E, FLINT-GARCIA S, GARCIA A, GLAUBITZ J C , et at. The genetic architecture of maize flowering time. Science, 2009,325(5941):714-718.
doi: 10.1126/science.1174276 |
[5] |
SWARTS K, GUTAKER R M, BENZ B, BLAKE M, BUKOWSKI R, HOLLAND J, KRUSE-PEEPLES M, LEPAK N, PRIM L, ROMAY M C , et at. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science, 2017,357(6350):512-515.
doi: 10.1126/science.aam9425 pmid: 28774930 |
[6] |
LU Y L, YAN J B, GUIMARAES C T, TABA S, HAO Z F, GAO S B, CHEN S J, LI J S, ZHANG S H, VIVEK B S , et at. Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theoretical and Applied Genetics, 2009,120(1):93-115.
doi: 10.1007/s00122-009-1162-7 pmid: 19823800 |
[7] |
TALLURY S, GOODMAN M . Experimental evaluation of the potential of tropical germplasm for temperate maize improvement. Theoretical and Applied Genetics, 1999,98(1):54-61.
doi: 10.1007/s001220051039 |
[8] |
HALLAUER A R, CARENA M J . Adaptation of tropical maize germplasm to temperate environments. Euphytica, 2013,196(1):1-11.
doi: 10.1007/s10681-013-1017-9 |
[9] |
KIMURA M . Evolutionary rate at the molecular level. Nature, 1968,217(5129):624-626.
doi: 10.1038/217624a0 |
[10] |
SMITH J M, HAIGH J . The hitch-hiking effect of a favourable gene. Genetics Research, 1974,23(1):23-35.
doi: 10.1017/S0016672300014634 pmid: 4407212 |
[11] |
TAJIMA F . Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989,123(3):585-595.
doi: 10.1101/gad.3.11.1801 pmid: 2513255 |
[12] |
NIELSEN R, WILLIAMSON S, KIM Y, HUBISZ M J, CLARK A G, BUSTAMANTE C . Genomic scans for selective sweeps using SNP data. Genome Research, 2005,15(11):1566-1575.
doi: 10.1101/gr.4252305 pmid: 16251466 |
[13] |
SABETI P C, REICH D E, HIGGINS J M, LEVINE H Z, RICHTER D J, SCHAFFNER S F, GABRIEL S B, PLATKO J V, PATTERSON N J, MCDONALD G J , et at. Detecting recent positive selection in the human genome from haplotype structure. Nature, 2002,419(6909):832.
doi: 10.1038/nature01140 pmid: 12397357 |
[14] |
VOIGHT B F, KUDARAVALLI S, WEN X Q, PRITCHARD J K . A map of recent positive selection in the human genome. PLoS Biology, 2006,4(3):e72.
doi: 10.1371/journal.pbio.0040072 pmid: 1892825 |
[15] |
SABETI P C, VARILLY P, FRY B, LOHMUELLER J, HOSTETTER E, COTSAPAS C, XIE X, BYRNE E H, MCCARROLL S A , et at. Genome-wide detection and characterization of positive selection in human populations. Nature, 2007,449(7164):913.
doi: 10.1038/nature06250 |
[16] |
WRIGHT S . The genetical structure of populations. Annals of Eugenics, 1949,15(1):323-354.
doi: 10.1007/978-3-642-88415-3 |
[17] |
WEIR B S, COCKERHAM C C . Estimating F-statistics for the analysis of population structure. Evolution, 1984,38(6):1358-1370.
doi: 10.1111/j.1558-5646.1984.tb05657.x pmid: 28563791 |
[18] |
GIANOLA D, SIMIANER H, QANBARI S . A two-step method for detecting selection signatures using genetic markers. Genetics Research, 2010,92(2):141-155.
doi: 10.1017/S0016672310000121 pmid: 20515517 |
[19] |
AXELSSON E, RATNAKUMAR A, ARENDT M L, MAQBOOL K, WEBSTER M T, Perloski M, Liberg O, ARNEMO J M, HEDHAMMAR A, LINDBLAD-TOH K . The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature, 2013,495(7441):360.
doi: 10.1038/nature11837 |
[20] |
LIU K J, GOODMAN M, MUSE S, SMITH J S, BUCKLER E, DOEBLEY J . Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics, 2003,165(4):2117-2128.
doi: 10.1017/S001667230006426 pmid: 14704191 |
[21] |
HE C, FU J J, ZHANG J, Li Y X, ZHENG J, ZHANG H W, YANG X H, WANG J H, WANG G Y . A gene-oriented haplotype comparison reveals recently selected genomic regions in temperate and tropical maize germplasm. PLoS ONE, 2017,12(1):e0169806.
doi: 10.1371/journal.pone.0169806 pmid: 5242465 |
[22] |
SCHNABLE P S, WARE D, FULTON R S, STEIN J C, WEI F S, PASTERNAK S, LIANG C Z, ZHANG J W, FULTON L, GRAVES T A , et at. The B73 maize genome: complexity, diversity, and dynamics. Science, 2009,326(5956):1112-1115.
doi: 10.1126/science.1178534 |
[23] |
JIAO Y P, PELUSO P, SHI J H, LIANG T, STITZER M C, WANG B, CAMPBELL M S, STEIN J C, WEI X H, CHIN C S , et at. Improved maize reference genome with single-molecule technologies. Nature, 2017,546(7659):524.
doi: 10.1038/nature22971 pmid: 28605751 |
[24] |
CHIA J M, SONG C, BRADBURY P J, COSTICH D, DE LEON N, DOEBLEY J, ELSHIRE R J, GAUT B, GELLER L, GLAUBITZ J C , et at. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics, 2012,44(7):803.
doi: 10.1038/ng.2313 |
[25] |
BUKOWSKI R, GUO X S, LU Y L, ZOU C, HE B, RONG Z Q, WANG B, XU D W, YANG B C, XIE C X , et at. Construction of the third-generation Zea mays haplotype map. GigaScience, 2017, 7(4): gix134.
doi: 10.1093/gigascience/gix134 pmid: 29300887 |
[26] |
DANECEK P, AUTON A, ABECASIS G, ALBERS C A, BANKS E, DEPRISTO M A, HANDSAKER R E, LUNTER G, MARTH G T, SHERRY S T , et at. 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics, 2011,27(15):2156-2158.
doi: 10.1093/bioinformatics/btr330 pmid: 21653522 |
[27] |
CINGOLANI P, PLATTS A, WANG L L, COON M, NGUYEN T, WANG L A, LAND S J, LU X Y, RUDEN D M . A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 2012,6(2):80-92.
doi: 10.4161/fly.19695 |
[28] |
MA Y, DING X, QANBARI S, WEIGEND S, ZHANG Q, SIMIANER H . Properties of different selection signature statistics and a new strategy for combining them. Heredity, 2015,115(5):426.
doi: 10.1038/hdy.2015.42 pmid: 4611237 |
[29] | HOAGLIN D C, MOSTELLER F, TUKEY J W . Understanding Robust and Exploratory Data Analysis. New York: John Wiley & Sons, 1983. |
[30] |
SZPIECH Z A, HERNANDEZ R D . selscan: An efficient multithreaded program to perform EHH-based scans for positive selection. Molecular Biology and Evolution, 2014,31(10):2824-2827.
doi: 10.1093/molbev/msu211 pmid: 4166924 |
[31] |
QUINLAN A R, HALL I M . BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 2010,26(6):841-842.
doi: 10.1093/bioinformatics/btq033 pmid: 20110278 |
[32] |
TIAN T, LIU Y, YAN H Y, YOU Q, YI X, DU Z, XU W Y, SU Z . AgriGO v2. 0: A GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research, 2017,45(W1):W122-W129.
doi: 10.1093/nar/gkx382 pmid: 28472432 |
[33] |
HUANG C, SUN H Y, XU D Y, LIANG Y M, WANG X F, XU G H, TIAN J G, WANG C L, LI D, WU L H , et at. ZmCCT9 enhances maize adaptation to higher latitudes. Proceedings of the National Academy of Sciences of the United States of America, 2018,115(2):E334-E341.
doi: 10.1073/pnas.1718058115 pmid: 29279404 |
[34] |
KHAN S, ROWE S C, HARMON F G . Coordination of the maize transcriptome by a conserved circadian clock. BMC Plant Biology, 2010,10(1):126.
doi: 10.1186/1471-2229-10-126 pmid: 20576144 |
[35] | GUO L, WANG X, ZHAO M, HUANG C, LI C, LI D, YANG C, YORK A M, XUE W, XU G, LIANG Y, CHEN Q, DOEBLEY J F, TIAN F . Stepwise cis-regulatory changes in ZCN8 contribute to maize flowering-time adaptation. Current Biology, 2018,28(18):3005-3015. |
[36] | MENG X, MUSZYNSKI M G, DANILEVSKAYA O N . The FT-like ZCN8 gene functions as a floral activator and is involved in photoperiod sensitivity in maize. The Plant Cell, 2011,23(3):942-960. |
[37] |
SHEEHAN M J, NACHMAN M W . Morphological and population genomic evidence that human faces have evolved to signal individual identity. Nature Communications, 2014,5:4800.
doi: 10.1038/ncomms5800 pmid: 25226282 |
[38] |
曾滔, 赵福平, 王光凯, 吴明明, 魏彩虹, 张莉, 李利, 张红平, 杜立新 . 基于群体分化指数FST的绵羊全基因组选择信号检测. 畜牧兽医学报, 2013,44(12):1891-1899.
doi: 10.11843/j.issn.0366-6964.2013.12.005 |
ZENG T, ZHAO F P, WANG G K, WU M M, WEI C H, ZHANG L, LI L, ZHANG H P, DU L X . Genome-wide detection of selection signatures in sheep populations with use of population differentiation index FST. Acta Veterinaria et Zootechnica Sinica, 2013,44(12):1891-1899. (in Chinese)
doi: 10.11843/j.issn.0366-6964.2013.12.005 |
|
[39] |
HUANG X, SANG T, ZHAO Q, QI F, ZHAO Y, LI C Y ZHU C R, LU T T, ZHANG Z W, LI M , et at. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 2010,42(11):961.
doi: 10.1038/ng.695 pmid: 20972439 |
[40] |
MCVICKER G, GORDON D, DAVIS C, GREEN P . Widespread genomic signatures of natural selection in hominid evolution. PLoS Genetics, 2009,5(5):e1000471.
doi: 10.1371/journal.pgen.1000471 pmid: 19424416 |
[41] | 薛周舣源, 宋显威, 吴林慧, 王露珍, 崔家安, 孙章健, 张政, 马云龙 . 畜禽选择信号检测方法及其统计学问题. 畜牧兽医学报, 2018,49(6):1099-1107. |
XUE Z Y Y, SONG X W, WU L H, WANG L Z, CUI J A, SUN Z J, ZHANG Z, MA Y L . The identification methods of selection signatures in livestock and its statistical problems. Acta Veterinaria et Zootechnica Sinica, 2018,49(6):1099-1107. (in Chinese) | |
[42] |
KUMAR I, SWAMINATHAN K, HUDSON K, HUDSON M E . Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling. Journal of Experimental Botany, 2016,67(14):4231-4240.
doi: 10.1093/jxb/erw217 pmid: 27262126 |
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