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Электронный журнал
Electronic Journal
УДК 634.11:575
1Ван де Вег В. Эрик, PhD
1Роланд Е. Форрипс, PhD
2Йоханнес В. Крайселбринк, PhD
2Ханс Янсен, PhD
3А. В. Пикунова, к.с.-х.н.
3З. М. Серова, к.с.-х.н.
3Н. Г. Красова, к.с.-х.н.
3Е. Н. Седов, к.с.-х.н.
4Фраунсуа Лорен, PhD
2Марко А.С.М. Бинк, PhD
1Вагенингенский университет и научно-исследовательский центр - Селекция растений, Нидерланды, Вагенинген, eric.vandeweg@wur.nl
2Вагенингенский университет и научно-исследовательский центр - Биометрия, Нидерланды, Вагенинген, marco.bink@wur.nl
3ФГБНУ ВНИИ селекции плодовых культур, Россия, Орел, info@vniispk.ru 4 НИИ Садоводства и семеноводства, Франция, Анже, francois.laurens@angers.inra.fr
Использование молекулярно-генетического анализа, основанного на родословных, в селекции и в качестве эффективного метода выявления локусов количественных признаков у селекционного материала с известным
происхождением
Аннотация
Молекулярно-генетический анализ родословных (Pedigree based analysis - PBA) является инновационным и мощным методом для обнаружения и характеристики связей между молекулярным маркером и фенотипическим признаком для дальнейшего использования в маркер вспомогательной селекции.
Статистические методы и программное обеспечение были проверены путем комплексного исследования на 27 семьях из пяти селекционных программ четырех стран [1], некоторые результаты представлены на рисунках 1 и 2. На рисунке 1 показаны позиции локусов количественных признаков (ЛКП) плотности плода после двух месяцев холодного хранения. На рисунке 2 локусы количественных признаков у 33 сортов и форм. Полученные данные могут быть использованы в селекционной работе как для подбора родительских пар для скрещивания так и для выбора целевых локусов количественных признаков. Локус картированный на группе сцепления 15 является перспективным для разработки маркера для дальнейшего использования в маркер вспомогательной селекции.
Селекционная программа по яблоне реализуемая во ВНИИСПК позволила получить целый ряд плодоносящих семей. В настоящее время ряд родителей этих
Электронный журнал
Electronic Journal
семей, а так же некоторые другие сорта были генотипированы с помощью Infinium® 20K SNP маркеров. Первые результаты дали информацию о генетическом разнообразии и родословных. Кроме того, в российских селекционных программах используются родители и предшественники общие с изучаемыми в совместном международном проекте FruitBreedomics. Все это может стать основой для сотрудничества с применением PBA методов.
Ключевые слова: маркер вспомогательная селекция, однонуклеотидные полиморфные маркеры (SNP), генотипирование, Rosaceae, Malus domestica
UDC 634.11:576.354.4
1 Van de Weg W. Eric, PhD
1 Roeland E. Voorrips, PhD
2 Johannes W. Kruisselbrink, PhD 2Hans Jansen, PhD
3Anna Pikunova, candidate of agricultural sciences (PhD) 3Zoya Serova, candidate of agricultural sciences (PhD) 3Nina Krasova, doctor of agricultural sciences 4Evgeny Sedov, doctor of agricultural sciences 4François Laurens, PhD 2Marco А.С.М. Bink, PhD
1Wageningen UR Plant Breeding, Droevendaalsesteeg 1, P.O. Box 386, 6700AJ, Wageningen, The Netherlands, eric.vandeweg@wur.n
2 Wageningen UR, Biometris, Droevendaalsesteeg 1, P.O. Box 16, 6700AA, Wageningen, The Netherlands, marco.bink@wur.nl 3Russian Research Institute of Fruit Crop Breeding, Russia, Orel, info@vniispk.ru
4UMR1345 Institut de Recherche en Horticulture et Semences, AgroCampus-Ouest, 49045 Angers, France, e-mail : francois. laurens@angers. inra.fr
Pedigree Based Analyses: A powerful approach for QTL discovery in pedigreed
breeding germplasm and support on breeding decisions
Abstract
Pedigree Based Analysis (PBA) is an innovative and powerful approach for the discovery and characterisation of marker-trait associations for use in marker assisted breeding. The power of PBA comes from the simultaneous analysis of multiple segregating full sib families, the use of breeding germplasm, and the use of known genetic relationships. The use of multiple families allows representation of wide genetic diversity thus increasing probability that desired genes/alleles are presented and segregating. This also allows examination of QTL performance across different genetic backgrounds, thus providing knowledge on the general applicability of results. Finally, the use of multiple families
increases the population size and thereby the statistical power. The use of breeding germplasm of ongoing breeding activities makes results directly applicable and relevant to the breeder and also reduces experimental costs since plant materials and part of the phenotypic measurements are already available. Finally, PBA provides a framework for extending the population and phenotypic data in time, thereby further strengthening statistical power.
The statistical approaches and software have been validated through an integrated study on 27 families from five breeding programs from four countries [1] from which some results are presented in figures 1 &2. Current PBA software includes FlexQTLTM for QTL discovery and characterization [1], Pedimap for the graphical presentation [2], Visual-FQ, which provides structured guidance through the analyses and FQ-haplotyper which assigns alleles to haploblocks (sets of tightly linked SNP markers).
Key words: marker assisted breeding, marker assisted selection, marker-trait associations SNP, genotyping, Rosaceae, Malus domestica
The above mentioned validation study in apple included only 87 SSR markers [1]. The current availability of high-throughput SNP genotyping infrastructures allows marker genotyping at much higher densities, which will contribute to higher mapping resolution and more accurate QTL characterization. FlexQTLTM has recently been adapted to such large scale SNP data. Also, FQ-haplotyper software has been developed, which builds highly informative multi-allelic haplotypes comprising consecutive lowly-informative SNPs, thus reducing dataset sizes and computation time without giving in on marker information while also increasing informativeness of single markers beyond that of SSR markers (Fig. 3). Indeed prospects for PBA on Rosaceae have dramatically increased through the availability of SNP arrays for high throughput genome wide genotyping [3, 4, 5, 6, 7], of pipelines for the processing of these SNP data into reliable genotype calls [http://compbiotoolbox.fmach.it/assist/], of strategies for composing study germplasm [9] and through the continuous decreasing prices for these arrays. To date, PBA has been embraced by several international and national research programs on apple, peach [9], cherry, strawberry and grape, and wheat and oil palm projects are expected to join soon. In apple, PBA-studies are in progress on, amongst others, fruit firmness, titratable acidity, Brix, crispness, juiciness, aroma, fruit size, fruit color, fruit over color, harvest data, and crop load within the framework of the European project FruitBreedomics [10].
VNIIISPK's apple breeding program has many fruit bearing families. Currently various of its breeding parents and some other Russian cultivars are being genotyped with the Infinium® 20K SNP array [6]. First results indicated the applicability of the array on Russian germplasm, thus providing information on the available genetic diversity and pedigree records [Fig. 3, 11]. Moreover, VNIIISPK and other Russian breeding programs have parents and or progenitors in common with the FruitBreedomics study population (Fig. 3). All this could be the prelude to a multi-institution PBA study in Russia with links to European and American PBA studies.
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Figure 1 - Probable QTL positions for fruit firmness after two months of cold storage following a PBA analyses on 27 full sib families
The starts and ends of chromosomes are indicated by dashed vertical lines. Peaks present the most probable position of QTLs. The probability of the presence of a true QTL on a linkage group (LG) is reflected by Bayes Factors (BFs). The 2lnBFs for the presence of one over no QTL are presented on top of each peak. A value greater than 5 and 10 indicate strong and decisive evidence respectively. This analysis gave no strong evidence for the presence of two QTL on a single LG. These data thus give at least strong evidence for the presence of six QTL. Data are taken from Bink et al. 2014 [1] for their additive QTL model with the Poisson prior distribution E(NQTL) = 5. ("Q5_R0").
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Figure 2 - Estimates of QTL genotype for the 33 parents of the full sib families
Estimates are plotted for those chromosome regions with at least strong (2lnBF10 > 5) for QTL presence (as presented in Fig. 1). The starts and ends of chromosomes are indicated by dashed vertical lines, and marker positions are indicated by inner ticks at the horizontal axis.
The blue, green and red colors indicate positive evidence for QTL genotypes qq(—), Qq(+-) and QQ(++), respectively. The grey color indicates ignorable evidence for any genotype).
Data are taken from Bink et al. 2014 [1] for their additive QTL model with the Poisson prior distribution E(NQTL) = 5 ("Q5_R0"). This QTL genotype information can be used in breeding decisions, like for the choice of parents for new crosses and for the QTL to target. The QTL on LG15 seems to be homozygous for the favourable allele for most parents. This may reflect high selection intensity and thereby the importance of this QTL. Also, due to the high level of homozygosity, development and use of markers may not be very cost efficient, especially in case of single marker tests.
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Figure 3 - Flow of haploblock alleles over six successive generations from the founder Antonovka Obyknovennaya to four progenies that are part of the QTL mapping study of Fig. 1 & 2 and that are also part of a larger mapping population of 45 individuals, and to two
Russian cultivars. Female parentage is indicated by pink and male parentage by blue lines. The two columns within a box indicate homologous chromosome segments. The two numbers
within a row indicate the two alleles within a haploblock locus. The three presented haploblock-loci cover the first 4cM of linkage group 12 of apple and comprise nine, seven and
ten SNP markers respectively
Antonovka's haplotype 9-2-3 was passed to the German Breeding selection B VIII 34.16 [11] to the breeding selection Z185 of Wageningen UR, The Netherlands, to two breeding selections of INRA-Angers, France, and finally segregates in a full-sib family of INRA-Angers. Actually, a full LG12-chromosome of Antonovka OB was passed to this family (data not shown), due to which QTL results for this chromosome could be transferable to Russian germplasm. Other Russian breeding germplasm that are in the pedigree of mapping populations of the FruitBreedomics [10] are Borowitsky (= Charlamowsky), and R12740-7A. On the other hand, Russian breeding programs used western cultivars that are now studied in FruitBreedomics like McIntosh and Wealthy.
Finally, the presented marker data also confirm the pedigree records of Morozovskoe and Orlovskoe Zimnee.
Acknowledgements
Proof of concept and the development of statistical approaches and software has been carried out with financial support from the Commission of the European Communities, specific research program "Quality of Life and Management of Living Resource", QLK5-2002-01492 "High-quality Disease Resistant Apples for a Sustainable Agriculture", the EU seventh Framework Programme by the FruitBreedomics project N°. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com), and by the USDA-NIFA-SCRI project RosBREED: Enabling marker-assisted breeding in Rosaceae (2009-51181-05808; http://www.rosbreed.org).
References
1. Bink MCAM, Jansen J, Madduri M, Voorrips RE, Durel C-E, Kouassi AB, Laurens F, Mathis F, Gessler C, Gobbin D, Rezzonico F, Patocchi A, Kellerhals M, Boudichevskaia A, Dunemann F, Peil A, Nowicka A, Lata B, Stankiewicz-Kosyl M, Jeziorek K, Pitera E, Soska A, Tomala K, Evans KM, Fernández-Fernández F, Guerra W, Korbin M, Keller S, Lewandowski M, Plocharski W, Rutkowski K, Zurawicz E, Costa F, Sansavini S, Tartarini S, Komjanc M, Mott D, Antofie A, Lateur M, Rondia A, Gianfranceschi L, van de Weg WE (2014): Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor Appl. Genet., 127:1073-1090. DOI 10.1007/s00122-014-2281-3
2. Voorrips RE, Bink MCAM, Van de Weg WE (2012): PEDIMAP: Software for the visualization of genetic and phenotypic data in pedigrees. J. Heredity, 103:903-907, DOI 10.1093/jhered/ess060
3. Chagné D., Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, VelascoR, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, van de Weg WE, Gardiner SE, Bassil N, Peace C (2012): Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE, 7(2):e31745. DOI: 10.1371/journal.pone.0031745
4. Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni E, Morgante M, Peace C Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm (2012): PLoS ONE, 7(4): e35668. DOI: 10.1371/journal.pone.0035668
5. Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A (2012): Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS ONE, 7(12):e48305. DOI: 10.1371/journal.pone.0048305
6. Bianco L, Cestaro A, Sargent DJ, BanchiE, Derdak S, Di Guardo N, Salvi S, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M. (2014): Development and validation of a 20K Single Nucleotide Polymorphism (SNP) whole genome genotyping array for apple (Malus x domestica Borkh). PLoS ONE, 9(10): e110377. doi:10.1371/journal.pone.0110377
7. Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood
D, Alperin ES, Rosyara UR, Koehorst-van Putten HJJ, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E (2015): Development and Preliminary Evaluation of a 90K Axiom® SNP Array in the Allo-octoploid Cultivated Strawberry Fragaria xananassa. BMC Genomics, 16:155. Doi:10.1186/s12864-015-1310-1
8. Peace C, Luby J, van de Weg E, Bink M, Iezzoni A (2014): A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry. Tree Gen Genom., 10: 1679-1694. DOI 10.1007/s11295-014-0788-z
9. Rosyara UR, Bink MCAM, van de Weg E, Zhang G, Sebolt A, Dirlewanger E, Quero-Garcia J, Schuster M, Iezzoni AF (2013): Fruit size QTL identification and the prediction of parental QTL genotypes and breeding values in multiple pedigreed populations of sweet cherry. Molecular Breeding, 32:875-887. DOI 10.1007/s11032-013-9916-y
10. Laurens F, Durel CE, Patocchi A, Peil A, Salvi S, Tartarini S, Velasco R, Weg van de E (2010): Review on apple genetics and breeding programmes and presentation of a new European initiative to increase fruit breeding efficiency. J Fruit Sci, 27: 102-107
11. Pikunova A, Madduri M, Sedov E, Noordijk Y, Peil A, Troggio M, Bus VGM, Visser RGF, van de Weg E (2013): 'Schmidt's Antonovka' is identical to 'Common Antonovka', an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses. Tree Gen. Genom. 10:261-271. DOI 10.1007/s11295-013-0679-8.
Литература
1. Bink MCAM. Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple / Bink MCAM, Jansen J, Madduri M, Voorrips RE, Durel C-E, Kouassi AB, Laurens F, Mathis F, Gessler C, Gobbin D, Rezzonico F, Patocchi A, Kellerhals M, Boudichevskaia A, Dunemann F, Peil A, Nowicka A, Lata B, Stankiewicz-Kosyl M, Jeziorek K, Pitera E, Soska A, Tomala K, Evans KM, Fernández-Fernández F, Guerra W, Korbin M, Keller S, Lewandowski M, Plocharski W, Rutkowski K, Zurawicz E, Costa F, Sansavini S, Tartarini S, Komjanc M, Mott D, Antofie A, Lateur M, Rondia A, Gianfranceschi L, van de Weg WE // Theor Appl. Genet. - 2014. - №127. - Р.1073-1090. DOI 10.1007/s00122-014-2281-3
2. Voorrips R.E. PEDIMAP: Software for the visualization of genetic and phenotypic data in pedigrees. / Voorrips R.E., Bink MCAM, Van de Weg WE // J. Heredity. - 2012. - №103. - Р.903-907. DOI 10.1093/jhered/ess060
3. Chagné D., Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. / Chagné D., Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, VelascoR, Main D, Rees JD, Iezzoni E, Mockler T, Wilhelm L, van de Weg WE, Gardiner SE, Bassil N, Peace C // PLoS ONE. - 2012. - №7(2). -е31745. DOI: 10.1371/journal.pone.0031745
4. Verde I. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. / Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin
E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni E, Morgante M, Peace C // PLoS ONE. - 2012. - №7(4). - e35668. DOI: 10.1371/journal.pone.0035668
Электронный журнал
Electronic Journal
5. Peace C. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. / Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A // PLoS ONE. - 2012. - №7(12). - e48305. DOI: 10.1371/journal.pone.0048305
6. Bianco L. Development and validation of a 20K Single Nucleotide Polymorphism (SNP) whole genome genotyping array for apple (Malus x domestica Borkh). / Bianco L, Cestaro A, Sargent DJ, BanchiE, Derdak S, Di Guardo N, Salvi S, Viola R, Gut I, Laurens F, Chagne D, Velasco R, van de Weg E, Troggio M. // PLoS ONE. - 2014. - №9(10). - e110377. doi:10.1371/journal.pone.0110377
7. Bassil N.V. Development and Preliminary Evaluation of a 90K Axiom® SNP Array in the Allo-octoploid Cultivated Strawberry Fragaria xananassa. / Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-van Putten HJJ, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E // BMC Genomics. - №16. - P.155. Doi:10.1186/s12864-015-1310-1
8. Peace C. A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry. / Peace C, Luby J, van de Weg E, Bink M, Iezzoni A // Tree Gen Genom. - 2014. - №10. - P.1679-1694. DOI 10.1007/s11295-014-0788-z
9. Rosyara UR. Fruit size QTL identification and the prediction of parental QTL genotypes and breeding values in multiple pedigreed populations of sweet cherry. / Rosyara UR, Bink MCAM, van de Weg E, Zhang G, Sebolt A, Dirlewanger E, Quero-Garcia J, Schuster M, Iezzoni AF // Molecular Breeding. - 2013. - №32. - P.875-887. DOI 10.1007/s11032-013-9916-y
10. Laurens F. Review on apple genetics and breeding programmes and presentation of a new European initiative to increase fruit breeding efficiency./ Laurens F, Durel CE, Patocchi A, Peil A, Salvi S, Tartarini S, Velasco R, van de Weg E // J. Fruit Sci. - 2010. - №27. - P.102-107.
11. Pikunova A. 'Schmidt's Antonovka' is identical to 'Common Antonovka', an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses. / Pikunova A, Madduri M, Sedov E, Noordijk Y, Peil A, Troggio M, Bus VGM, Visser RGF, van de Weg E (2013): // Tree Gen. Genom. - 2013. - №10. - P.261-271. DOI 10.1007/s11295-013-0679-8.
