[1] |
WU G A, TEROL J, IBANEZ V, LÓPEZ-GARCÍA A, PÉREZ- ROMÁN E, BORREDÁ C, DOMINGO C, TADEO F R, CARBONELL- CABALLERO J, ALONSO R, CURK F, DU D L, OLLITRAULT P, ROOSE M L, DOPAZO J, GMITTER F G, ROKHSAR D S, TALON M. Genomics of the origin and evolution of Citrus. Nature, 2018, 554(7692): 311-316.
doi: 10.1038/nature25447
|
[2] |
WANG X, XU Y T, ZHANG S Q, CAO L, HUANG Y, CHENG J F, WU G Z, TIAN S L, CHEN C L, LIU Y, YU H W, YANG X M, LAN H, WANG N, WANG L, XU J D, JIANG X L, XIE Z Z, TAN M L, LARKIN R M, CHEN L L, MA B G, RUAN Y J, DENG X X, XU Q. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nature Genetics, 2017, 49(5): 765-772.
doi: 10.1038/ng.3839
pmid: 28394353
|
[3] |
XU Q, CHEN L L, RUAN X A, CHEN D J, ZHU A D, CHEN C L, BERTRAND D, JIAO W B, HAO B H, LYON M P, CHEN J J, GAO S, XING F, LAN H, CHANG J W, GE X H, LEI Y, HU Q, MIAO Y, WANG L, XIAO S X, BISWAS M K, ZENG W F, GUO F, CAO H B, YANG X M, XU X W, CHENG Y J, XU J, LIU J H, LUO O J, TANG Z H, GUO W W, KUANG H H, ZHANG H Y, ROOSE M L, NAGARAJAN N, DENG X X, RUAN Y J. The draft genome of sweet orange (Citrus sinensis). Nature Genetics, 2013, 45(1): 59-66.
doi: 10.1038/ng.2472
pmid: 23179022
|
[4] |
WU G A, SUGIMOTO C, KINJO H, AZAMA C, MITSUBE F, TALON M, GMITTER F G, ROKHSAR D S. Diversification of mandarin citrus by hybrid speciation and apomixis. Nature Communications, 2021, 12(1): 4377.
doi: 10.1038/s41467-021-24653-0
pmid: 34312382
|
[5] |
BARKLEY N A, ROOSE M L, KRUEGER R R, FEDERICI C T. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theoretical and Applied Genetics, 2006, 112(8): 1519-1531.
doi: 10.1007/s00122-006-0255-9
pmid: 16699791
|
[6] |
DEMARCQ B, CAVAILLES M, LAMBERT L, SCHIPPA C, OLLITRAULT P, LURO F. Characterization of odor-active compounds of ichang lemon (Citrus wilsonii Tan.) and identification of its genetic interspecific origin by DNA genotyping. Journal of Agricultural and Food Chemistry, 2021, 69(10): 3175-3188.
doi: 10.1021/acs.jafc.0c07894
|
[7] |
GONZALEZ-IBEAS D, IBANEZ V, PEREZ-ROMAN E, BORREDÁ C, TEROL J, TALON M. Shaping the biology of citrus: II. Genomic determinants of domestication. The Plant Genome, 2021, 14(3): e20133.
|
[8] |
WU G A, PROCHNIK S, JENKINS J, SALSE J, HELLSTEN U, MURAT F, PERRIER X, RUIZ M, SCALABRIN S, TEROL J, et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology, 2014, 32(7): 656-662.
doi: 10.1038/nbt.2906
pmid: 24908277
|
[9] |
YU H W, YANG X M, GUO F, JIANG X L, DENG X X, XU Q. Genetic diversity and population structure of pummelo (Citrus maxima) germplasm in China. Tree Genetics & Genomes, 2017, 13(3): 58.
|
[10] |
刘勇, 刘德春, 吴波, 孙中海. 利用SSR标记对中国柚类资源及近缘种遗传多样性研究. 农业生物技术学报, 2006, 14(1): 90-95.
|
|
LIU Y, LIU D C, WU B, SUN Z H. Genetic diversity of pummelo and their relatives based on SSR markers. Journal of Agricultural Biotechnology, 2006, 14(1): 90-95. (in Chinese)
|
[11] |
ELSHIRE R J, GLAUBITZ J C, SUN Q, POLAND J A, KAWAMOTO K, BUCKLER E S, MITCHELL S E. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 2011, 6(5): e19379.
doi: 10.1371/journal.pone.0019379
|
[12] |
ISLAM A S M F, SANDERS D, MISHRA A K, JOSHI V. Genetic diversity and population structure analysis of the USDA olive germplasm using genotyping-by-sequencing (GBS). Genes, 2021, 12(12): 2007.
doi: 10.3390/genes12122007
|
[13] |
doi: 10.3864/j.issn.0578-1752.2017.09.012
|
|
WANG X K, JIANG D, SUN Z Z. Study on phylogeny of 240 mandarin accessions with genotyping-by-sequencing technology. Scientia Agricultura Sinica, 2017, 50(9): 1666-1673. doi: 10.3864/j.issn.0578-1752.2017.09.012. (in Chinese)
doi: 10.3864/j.issn.0578-1752.2017.09.012
|
[14] |
CHEN W, HOU L, ZHANG Z Y, PANG X M, LI Y Y. Genetic diversity, population structure, and linkage disequilibrium of a core collection of Ziziphus jujuba assessed with genome-wide SNPs developed by genotyping-by-sequencing and SSR markers. Frontiers in Plant Science, 2017, 8: 575.
|
[15] |
BIRD K A, AN H, GAZAVE E, GORE M A, PIRES J C, ROBERTSON L D, LABATE J A. Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L. Frontiers in Plant Science, 2017, 8: 321.
|
[16] |
ELTAHER S, SALLAM A, BELAMKAR V, EMARA H A, NOWER A A, SALEM K F M, POLAND J, BAENZIGER P S. Genetic diversity and population structure of F3:6 Nebraska winter wheat genotypes using genotyping-by-sequencing. Frontiers in Genetics, 2018, 9: 76.
doi: 10.3389/fgene.2018.00076
|
[17] |
ALIPOUR H, BIHAMTA M R, MOHAMMADI V, PEYGHAMBARI S A, BAI G H, ZHANG G R. Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Frontiers in Plant Science, 2017, 8: 1293.
doi: 10.3389/fpls.2017.01293
pmid: 28912785
|
[18] |
DELFINI J, MODA-CIRINO V, DOS SANTOS NETO J, RUAS P M, SANT'ANA G C, GEPTS P, GONÇALVES L S A. Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm. Scientific Reports, 2021, 11(1): 2964.
doi: 10.1038/s41598-021-82437-4
pmid: 33536468
|
[19] |
LUO Z N, BROCK J, DYER J M, KUTCHAN T, SCHACHTMAN D, AUGUSTIN M, GE Y F, FAHLGREN N, ABDEL-HALEEM H. Genetic diversity and population structure of a Camelina sativa spring panel. Frontiers in Plant Science, 2019, 10: 184.
doi: 10.3389/fpls.2019.00184
|
[20] |
HYUN D Y, SEBASTIN R, LEE G A, LEE K J, KIM S H, YOO E, LEE S, KANG M J, LEE S B, JANG I, RO N Y, CHO G T. Genome-wide SNP markers for genotypic and phenotypic differentiation of melon (Cucumis melo L.) varieties using genotyping- by-sequencing. International Journal of Molecular Sciences, 2021, 22(13): 6722.
doi: 10.3390/ijms22136722
|
[21] |
AKRAM S, ARIF M A R, HAMEED A. A GBS-based GWAS analysis of adaptability and yield traits in bread wheat (Triticum aestivum L.). Journal of Applied Genetics, 2021, 62(1): 27-41.
doi: 10.1007/s13353-020-00593-1
|
[22] |
POLAND J, ENDELMAN J, DAWSON J, RUTKOSKI J, WU S Y, MANES Y, DREISIGACKER S, CROSSA J, SÁNCHEZ-VILLEDA H, SORRELLS M, JANNINK J L. Genomic selection in wheat breeding using genotyping-by-sequencing. The Plant Genome, 2012, 5(3): 103-113.
|
[23] |
KAUR G, PATHAK M, SINGLA D, SHARMA A, CHHUNEJA P, SARAO N K. High-density GBS-based genetic linkage map construction and QTL identification associated with yellow mosaic disease resistance in bitter gourd (Momordica charantia L.). Frontiers in Plant Science, 2021, 12: 671620.
doi: 10.3389/fpls.2021.671620
|
[24] |
ABED A, BADEA A, BEATTIE A, KHANAL R, TUCKER J, BELZILE F. A high-resolution consensus linkage map for barley based on GBS-derived genotypes. Genome, 2022, 65(2): 83-94.
doi: 10.1139/gen-2021-0055
|
[25] |
VERMA S, GUPTA S, BANDHIWAL N, KUMAR T, BHARADWAJ C, BHATIA S. High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Scientific Reports, 2015, 5(1): 17512.
doi: 10.1038/srep17512
|
[26] |
POLAND J A, BROWN P J, SORRELLS M E, JANNINK J L. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE, 2012, 7(2): e32253.
doi: 10.1371/journal.pone.0032253
|
[27] |
GAUR R, VERMA S, PRADHAN S, AMBREEN H, BHATIA S. A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.). Functional & Integrative Genomics, 2020, 20(6): 763-773.
|
[28] |
WANG B Y, TAN H W, FANG W P, MEINHARDT L W, MISCHKE S, MATSUMOTO T, ZHANG D P. Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of Longan (Dimocarpus longan) germplasm. Horticulture Research, 2015, 2: 14065.
doi: 10.1038/hortres.2014.65
pmid: 26504559
|
[29] |
PEMBLETON L W, DRAYTON M C, BAIN M, BAILLIE R C, INCH C, SPANGENBERG G C, WANG J P, FORSTER J W, COGAN N O I. Targeted genotyping-by-sequencing permits cost- effective identification and discrimination of pasture grass species and cultivars. Theoretical and Applied Genetics, 2016, 129(5): 991-1005.
doi: 10.1007/s00122-016-2678-2
|
[30] |
STRAZZER P, SPELT C E, LI S J, BLIEK M, FEDERICI C T, ROOSE M L, KOES R, QUATTROCCHIO F M. Hyperacidification of Citrus fruits by a vacuolar proton-pumping P-ATPase complex. Nature Communications, 2019, 10(1): 744.
doi: 10.1038/s41467-019-08516-3
|
[31] |
LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25(14): 1754-1760.
doi: 10.1093/bioinformatics/btp324
pmid: 19451168
|
[32] |
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, MCVEAN G, DURBIN R, GROUP 1 G P A. The variant call format and VCFtools. Bioinformatics, 2011, 27(15): 2156-2158.
doi: 10.1093/bioinformatics/btr330
pmid: 21653522
|
[33] |
CHANG C C. Data management and summary statistics with PLINK. Methods in Molecular Biology, 2020, 2090: 49-65.
doi: 10.1007/978-1-0716-0199-0_3
pmid: 31975163
|
[34] |
MANICHAIKUL A, MYCHALECKYJ J C, RICH S S, DALY K, SALE M, CHEN W M. Robust relationship inference in genome-wide association studies. Bioinformatics, 2010, 26(22): 2867-2873.
doi: 10.1093/bioinformatics/btq559
pmid: 20926424
|
[35] |
PAN T F, ALI M M, GONG J M, SHE W Q, PAN D M, GUO Z X, YU Y, CHEN F X. Fruit physiology and sugar-acid profile of 24 pomelo (Citrus grandis (L.) osbeck) cultivars grown in subtropical region of China. Agronomy, 2021, 11(12): 2393.
doi: 10.3390/agronomy11122393
|
[36] |
D'AGOSTINO N, TARANTO F, CAMPOSEO S, MANGINI G, FANELLI V, GADALETA S, MIAZZI M M, PAVAN S, DI RIENZO V, SABETTA W, LOMBARDO L, ZELASCO S, PERRI E, LOTTI C, CIANI E, MONTEMURRO C. GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars. Scientific Reports, 2018, 8(1): 15877.
doi: 10.1038/s41598-018-34207-y
pmid: 30367101
|
[37] |
MEDINA R, WOGAN G O U, BI K, TERMIGNONI-GARCÍA F, BERNAL M H, JARAMILLO-CORREA J P, WANG I J, VÁZQUEZ- DOMÍNGUEZ E. Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog. Molecular Ecology, 2021, 30(16): 4062-4076.
doi: 10.1111/mec.v30.16
|
[38] |
何天富. 中国柚类栽培. 北京: 中国农业出版社, 1999.
|
|
HE T F. Cultivation of Pomelo in China. Beijing: China Agriculture Press, 1999. (in Chinese)
|
[39] |
BAAZAOUI I, MCEWAN J, ANDERSON R, BRAUNING R, MCCULLOCH A, VAN STIJN T, BEDHIAF-ROMDHANI S. GBS data identify pigmentation-specific genes of potential role in skin-photosensitization in two Tunisian sheep breeds. Animals, 2019, 10(1): 5.
doi: 10.3390/ani10010005
|
[40] |
ZHANG M M, YANG L, SU Z C, ZHU M Z, LI W T, WU K L, DENG X M. Genome-wide scan and analysis of positive selective signatures in Dwarf Brown-egg Layers and Silky Fowl chickens. Poultry Science, 2017, 96(12): 4158-4171.
doi: 10.3382/ps/pex239
pmid: 29053852
|
[41] |
NILO-POYANCO R, MORAGA C, BENEDETTO G, ORELLANA A, ALMEIDA A M. Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening. BMC Genomics, 2021, 22(1): 17.
doi: 10.1186/s12864-020-07299-y
|
[42] |
ZHENG B B, ZHAO L, JIANG X H, CHERONO S, LIU J J, OGUTU C, NTINI C, ZHANG X J, HAN Y P. Assessment of organic acid accumulation and its related genes in peach. Food Chemistry, 2021, 334: 127567.
doi: 10.1016/j.foodchem.2020.127567
|
[43] |
YE J, WANG X, HU T X, ZHANG F X, WANG B, LI C X, YANG T X, LI H X, LU Y E, GIOVANNONI J J, ZHANG Y Y, YE Z B. An InDel in the promoter of Al-ACTIVATED MALATE TRANSPORTER9 selected during tomato domestication determines fruit malate contents and aluminum tolerance. The Plant Cell, 2017, 29(9): 2249-2268.
doi: 10.1105/tpc.17.00211
|
[44] |
LI C L, DOUGHERTY L, COLUCCIO A E, MENG D, EL-SHARKAWY I, BOREJSZA-WYSOCKA E, LIANG D, PIÑEROS M A, XU K N, CHENG L L. Apple ALMT 9 requires a conserved C-terminal domain for malate transport underlying fruit acidity. Plant Physiology, 2020, 182(2): 992-1006.
doi: 10.1104/pp.19.01300
|
[45] |
DE ANGELI A, BAETZ U, FRANCISCO R, ZHANG J B, CHAVES M M, REGALADO A. The vacuolar channel VvALMT9 mediates malate and tartrate accumulation in berries of Vitis vinifera. Planta, 2013, 238(2): 283-291.
doi: 10.1007/s00425-013-1888-y
|