The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajanL.)

Background Pigeonpea (Cajanus cajan (L.) Millsp) is one of the major grain legume crops of the tropics and subtropics, but biotic stresses [Fusarium wilt (FW), sterility mosaic disease (SMD), etc.] are serious challenges for sustainable crop production. Modern genomic tools such as molecular markers and candidate genes associated with resistance to these stresses offer the possibility of facilitating pigeonpea breeding for improving biotic stress resistance. Availability of limited genomic resources, however, is a serious bottleneck to undertake molecular breeding in pigeonpea to develop superior genotypes with enhanced resistance to above mentioned biotic stresses. With an objective of enhancing genomic resources in pigeonpea, this study reports generation and analysis of comprehensive resource of FW- and SMD- responsive expressed sequence tags (ESTs). Results A total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ('ICPL 20102' and 'ICP 2376') and SMD ('ICP 7035' and 'TTB 7') and a total of 9,888 (9,468 high quality) ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231. Clustering and assembly analyses of these ESTs resulted into 4,557 unique sequences (unigenes) including 697 contigs and 3,860 singletons. BLASTN analysis of 4,557 unigenes showed a significant identity with ESTs of different legumes (23.2-60.3%), rice (28.3%), Arabidopsis (33.7%) and poplar (35.4%). As expected, pigeonpea ESTs are more closely related to soybean (60.3%) and cowpea ESTs (43.6%) than other plant ESTs. Similarly, BLASTX similarity results showed that only 1,603 (35.1%) out of 4,557 total unigenes correspond to known proteins in the UniProt database (≤ 1E-08). Functional categorization of the annotated unigenes sequences showed that 153 (3.3%) genes were assigned to cellular component category, 132 (2.8%) to biological process, and 132 (2.8%) in molecular function. Further, 19 genes were identified differentially expressed between FW- responsive genotypes and 20 between SMD- responsive genotypes. Generated ESTs were compiled together with 908 ESTs available in public domain, at the time of analysis, and a set of 5,085 unigenes were defined that were used for identification of molecular markers in pigeonpea. For instance, 3,583 simple sequence repeat (SSR) motifs were identified in 1,365 unigenes and 383 primer pairs were designed. Assessment of a set of 84 primer pairs on 40 elite pigeonpea lines showed polymorphism with 15 (28.8%) markers with an average of four alleles per marker and an average polymorphic information content (PIC) value of 0.40. Similarly, in silico mining of 133 contigs with ≥ 5 sequences detected 102 single nucleotide polymorphisms (SNPs) in 37 contigs. As an example, a set of 10 contigs were used for confirming in silico predicted SNPs in a set of four genotypes using wet lab experiments. Occurrence of SNPs were confirmed for all the 6 contigs for which scorable and sequenceable amplicons were generated. PCR amplicons were not obtained in case of 4 contigs. Recognition sites for restriction enzymes were identified for 102 SNPs in 37 contigs that indicates possibility of assaying SNPs in 37 genes using cleaved amplified polymorphic sequences (CAPS) assay. Conclusion The pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance. Sequence analyses of this dataset have showed conservation of a considerable number of pigeonpea transcripts across legume and model plant species analysed as well as some putative pigeonpea specific genes. Validation of identified biotic stress responsive genes should provide candidate genes for allele mining as well as candidate markers for molecular breeding

Wheat Genomics: Present Status and Future Prospects

Wheat (Triticum aestivum L.), with a large genome (16000 Mb) and high proportion (∼80%) of repetitive sequences, has been a difficult crop for genomics research. However, the availability of extensive cytogenetics stocks has been an asset, which facilitated significant progress in wheat genomic research in recent years. For instance, fairly dense molecular maps (both genetic and physical maps) and a large set of ESTs allowed genome-wide identification of gene-rich and gene-poor regions as well as QTL including eQTL. The availability of markers associated with major economic traits also allowed development of major programs on marker-assisted selection (MAS) in some countries, and facilitated map-based cloning of a number of genes/QTL. Resources for functional genomics including TILLING and RNA interference (RNAi) along with some new approaches like epigenetics and association mapping are also being successfully used for wheat genomics research. BAC/BIBAC libraries for the subgenome D and some individual chromosomes have also been prepared to facilitate sequencing of gene space. In this brief review, we discuss all these advances in some detail, and also describe briefly the available resources, which can be used for future genomics research in this important crop

Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.)

This study reports generation of large-scale genomic resources for pigeonpea, a so-called ‘orphan crop species’ of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)- and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW- and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes

Microsatellite Development and Application in Pigeonpea (<i>Cajanus cajan </i>(L.) Millsp.)

Pigeonpea is a major legume crop grown in the semi-arid tropics but has been relatively neglected in terms of genomic research. This study aimed at developing molecular markers as a basic requirement towards initiating marker assisted breeding techniques in pigeonpea. Simple Sequence Repeat (SSR) loci of pigeonpea were isolated by screening non-enriched (library A) and enriched (library B) partial genomic libraries with SSR probes. Positive clones were sequenced and primers designed for 152 microsatellite loci, 39 from library A and 113 from library B. Optimisation of reaction conditions was achieved for 51% and 65% of primers designed from library A and B, respectively. For the purpose of exploiting the transferability of SSRs across genera within the legume species, 220 soybean primers were tested in pigeonpea, 39 of which amplified interpretable bands. Nineteen out of 20 amplified primers from library A were polymorphic among 15 cultivated and 9 wild species. The diversity analysis revealed contrasted levels of variability within cultivated and wild accessions. A total of 98 alleles were detected at the 19 polymorphic loci with an average of 4.9 alleles per locus while the observed heterozygosity ranged from 0.17 – 0.80 with a mean of 0.42 per locus. Substantially less allelic variation (31 alleles) was observed within the cultivated species than across the wild species (92 alleles). Primers from library B were not tested for amplification in wild species but 35 out of the amplified 73 revealed polymorphism among 24 pigeonpea genotypes. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. Only one of the 39 amplified soybean primers revealed polymorphism among 24 cultivated pigeonpea accessions. No significant relationship was detected between the class of repeats and heterozygosity values. AT and TG class of repeats were the most abundant di-nucleotide repeats in library A and B respectively while TAA and GAA were the most abundant trinucleotide repeats in both libraries. Protein database searches provided putative functions for 21 SSR-containing pigeonpea sequences that would be useful in functional marker development. UPGMA and MDS cluster analysis revealed genetic relationships among recently bred varieties, old varieties and wild accessions. Nine of the markers developed were polymorphic to the parental lines of a F6 Fusarium wilt RIL mapping population that had been developed by ICRISAT breeders. Analysis of allele segregation in the RIL population revealed that all the 9 SSRs segregated in the expected 1:1 ratio and were further tested for any possible linkage with a QTL for resistance to Fusarium wilt. All the polymorphic markers derived from this study are now being used for characterisation and evaluation of pigeonpea germplasm collection at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) headquarters, India. SSRs provide a powerful tool for genomic studies and are recommended for systematic fingerprinting of pigeonpea germplasm

Sequencing the Major Mycosphaerella Pathogens of Wheat and Banana

Mycosphaerella is one of the largest genera of plant-pathogenic fungi with more than 1,000 named species, many of which are important pathogens causing leaf spotting diseases in a wide variety of crops including cereals, citrus, banana, eucalypts, soft fruits and horticultural crops. A few species of Mycosphaerella cause disease in humans and other vertebrates. An international project was initiated to sequence the genomes of M. graminicola and M. fijiensis, two of the most economically important pathogens of wheat and banana, respectively, along with 40,000 ESTs from M. fijiensis and the related maize pathogen Cercospora zeae-maydis. The 9x M. graminicola genome size is 39.8 Mb with chromosome sizes from 548 kb to 6 Mb and a complete circular mitochondrial genome of 43,947 bp. Our data indicate that M. graminicola has both the largest chromosome number and the smallest chromosome sizes recorded among filamentous ascomycetes. The Mycosphaerella Genomics Consortium, which was established in 2003, decided to use M. graminicola as the model to develop more genetic and genomic research on M. fijiensis. Since 2003, M. fijiensis EST sequencing has resulted in more than 30,000 ESTs, and the genome sequencing was recently finished at 7.8x. The genome size of M. fijiensis is 80% larger than that of M. graminicola. The completed mitochondrial sequence is more then twice as large, and the estimated nuclear genome size is approximately 72 Mb. The extension of the genome size of M. fijiensis seems to be mostly due to additional repeated sequences. The status of Mycosphaerella sequencing will have a significant effect on future studies aimed at the control of black leaf streak disease. The current status of both sequencing projects and other initiatives to exploit this information and to put it into a multidisciplinary approach focusing on sustainable management of the disease will be discusse

Utilization of tall wheatgrass translocation lines to improve fusarium head blight resistance in wheat

Fusarium head blight (FHB) and leaf rust (LR) are two major fungal pathogens threatening the wheat crop, consequently identifying resistance genes from various sources is always of importance to wheat breeders. Type II FHB resistance in wheat has been improved by introgressing QTL from landraces and wild species. The present study was undertaken to (1) combine two different type II FHB resistance QTL in the backgrounds of six adapted wheat lines (2) improve the map resolution of Qfhs.pur-7EL.^ In the first objective, the FHB resistance gene Fhb1 originated in a Chinese wheat cultivar and is located on wheat chromosome 3BS, and Qfhs.pur-7ELwas introgressed from tall wheatgrass onto wheat chromosome 7DL were combined in six adapted wheat lines. The effect of pyramiding resistance genes through marker-assisted selection was assessed by scoring plants for disease development after inoculating with a combination of four different local FHB isolates. The response of 6 populations of pyramided lines was evaluated in both greenhouse and transplant nursery. The pyramided lines as well as Fhb1-only lines exhibited high levels of resistance to the mixture of four FHB isolates. Although Fhb1 or Qfhs.pur-7EL alone is strong enough to achieve satisfactory resistance, pyramided lines may be more stable over time.^ In the second objective, we identified tightly linked markers for FHB-resistance QTL Qfhs.pur-7EL and the LR-resistance gene Lr19 using genotyping by sequencing in a wheat-tall wheatgrass introgression-derived recombinant inbred line (RIL) population. 216,318 SNPs were discovered for this population. After filtering, 1700 high-confidence SNPs were used to conduct the linkage and QTL analysis. Qfhs.pur-7EL was mapped to a 2.9 cM region within a 43.6 cM segment of wheatgrass chromosome 7el 2 that was translocated onto wheat chromosome 7DL. The LR gene Lr19 from 7el1 was mapped to a 1.21 cM region in the same area, in repulsion. Five lines were identified with the resistance-associated SNP alleles in coupling for Qfhs.pur-7EL and Lr19. Investigation of the genetic characteristics of the parental lines of this RIL population indicated that they are translocation lines in two different wheat cultivar genetic backgrounds instead of 7E-7D substitution lines in Thatcher wheat background as previously reported in the literature. ^ The wheat lines containing pyramided FHB resistance genes and pyramided FHB and LR resistance genes: Qfhs.pur-7EL and Lr19, developed and identified in this study, show potential as genetic resources for sustainable wheat production in areas affected by Fusarium head blight and leaf rust diseases

Generation of Expressed Sequence Tags and Marker Development for Sterility Mosaic Disease Resistance in Pigeonpea

Sterility mosaic disease (SMD), an important biotic constraint on pigeonpea (Cajanus cajan (L) Millsp.) in the Indian subcontinent, is caused by Pigeonpea sterility mosaic virus and transmitted by the eriophyid mite. Investigations were carried out to develop F2:3 mapping population involving resistant (ICP 7035) and susceptible (TTB 7) parents, development of EST SSR markers, construction of linkage map and identification of QTLs for SMD resistance. F1s of the susceptible × resistant cross were susceptible indicating susceptibility to be dominant over resistance. The pattern of frequency distribution of SMD incidence in the F2:3 was found to be continuous depicting quantitative nature of resistance. Totally 3,788 high quality ESTs were generated from SMD challenged genotypes of ICP 7035 and TTB 7. Sequence clustering and assembly process of all the assembled 3,788 ESTs resulted in 1,308 unigenes. Out of 3320 SSR markers (3236 genomic+84 genic) screened for SMD in TTB 7 and ICP 7035, 2107 (63.5%) could amplify and 84 (83 genomic + 01 genic) SSR markers were found to be polymorphic (2.5%). A total of 82 markers were mapped on 11 linkage groups (LGs) of pigeonpea spanning 539.5 cM and two markers remained ungrouped. Number of markers mapped per linkage group ranged from three (LG 11) to twelve (LG 7). The present study yielded two QTLs for Bengaluru isolate of SMD positioned on LG 3 and LG 7 accounting 10.39 per cent and 15.74 of the phenotypic variation respectively. For Patancheru isolate also, two QTLs were identified and the first QTL explained 12.3 per cent phenotypic variation and the second QTL explained 24.69 per cent of phenotypic variation

Multiple Minor QTLs Are Responsible for Fusarium Head Blight Resistance in Chinese Wheat Landrace Haiyanzhong

Citation: Cai, Jin, Shan Wang, Tao Li, Guorong Zhang, and Guihua Bai. “Multiple Minor QTLs Are Responsible for Fusarium Head Blight Resistance in Chinese Wheat Landrace Haiyanzhong.” Edited by Maoteng Li. PLOS ONE 11, no. 9 (September 27, 2016): e0163292. https://doi.org/10.1371/journal.pone.0163292.Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, is a devastating disease in wheat (Triticum aestivum L.). Use of host resistance is one of the most effective strategies to minimize the disease damage. Haiyanzhong (HYZ) is a Chinese wheat landrace that shows a high level of resistance to FHB spread within a spike (type II resistance). To map the quantitative trait loci (QTLs) in HYZ and identify markers tightly linked to the QTLs for FHB resistance, a population of 172 recombinant inbred lines (RILs) from a cross between HYZ and Wheaton (FHB susceptible) was genotyped using simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs) derived from genotyping-bysequencing (GBS), and evaluated for percentage of symptomatic spikelets (PSSs) per spike in three greenhouse experiments. Six QTLs for type II resistance were identified in HYZ, indicating that multiple minor QTLs together can provide a high level of FHB resistance in wheat. The QTL with the largest effect on FHB resistance was mapped on the chromosome arm 5AS, and the other five from HYZ were mapped on the chromosomes 6B, 7D, 3B, 4B and 4D. In addition, two QTLs from Wheaton were mapped on 2B. Critical SNPs linked to the QTLs on chromosomes 5A, 6B, and 2B were converted into KBioscience competitive allele-specific PCR (KASP) assays, which can be used for marker-assisted selection (MAS) to pyramid these QTLs in whea

GENETICS AND GENOMICS OF CULTIVATED EGGPLANTS AND WILD RELATIVES

Tesis por compendioAlimentar a la futura población en crecimiento en un contexto de cambio climático exige nuevos enfoques y herramientas de mejora genética para desarrollar nuevas variedades de cultivos que sean resilientes y eficientes en el uso de los recursos. Entre las hortalizas, la berenjena (Solanum melongena) es reconocida como un cultivo importante y como tal está incluida en el Anexo 1 del Tratado Internacional sobre los Recursos Fitogenéticos para la Alimentación y la Agricultura, que incluye 34 cultivos considerados como los más relevantes para la humanidad. Antes del inicio de esta tesis, se disponía de pocas herramientas genéticas y genómicas para la mejora genética de la berenjena, las cuales se revisan en un capítulo introductorio. Asimismo, hemos reconocido la importancia de los parientes silvestres de la berenjena, que apenas se han utilizado en la mejora genética de la misma. A este respecto, para hacer un uso más eficiente de los parientes silvestres en la mejora genética, propusimos un enfoque ambicioso, llamado "introgressiomics", que consiste en un desarrollo sistemático y masivo de materiales que lleven introgresiones de parientes silvestres (CWR), los cuales generalmente son una fuente inexplorada e desaprovechada de variación genética. Los trabajos realizados en esta tesis están relacionados con la aplicación de este enfoque a la berenjena. En este marco, los objetivos generales de la tesis son el desarrollo de la información y herramientas genéticas y genómicas en el acervo genético de la berenjena, utilizando un enfoque multidisciplinario y multifacético para la mejora genética en el desarrollo de nuevas variedades mejoradas y resistentes usando especies relacionadas como fuente de variación. Concretamente, en el primer capítulo de esta tesis, secuenciamos el transcriptoma de dos especies relacionadas con la berenjena, la silvestre Solanum incanum y la especie cultivada africana S. aethiopicum, que tienen un gran interés en la mejora genética de la berenjena. Los transcriptomas se ensamblaron en 83,905 y 87,084 unigenes para S. incanum y S. aethiopicum respectivamente, los cuales fueron extensivamente anotados estructuralmente y funcionalmente. La busqueda de variantes alélicas identificó decenas de miles de polimorfismos intraespecíficos e interespecíficos, así como alrededor de un millar de SSRs en cada especie. En el segundo capítulo, un subconjunto de esos marcadores (11 SSRs y 35 SNPs) se analizaron para confirmar su utilidad para la huella genética, la evaluación de la diversidad y el establecimiento de relaciones entre las berenjenas cultivadas (común, escarlata y gboma). Observamos que los SSRs y los SNPs proporcionaron resultados diferentes en el establecimiento de las relaciones, lo que sugiere que cada tipo de marcador muestreó diferentes niveles de variación genética. Sin embargo, aunque ambos marcadores proporcionaron un nivel similar de información, los SNPs parecen proporcionar una mejor resolución que los SSRs para materiales filogenéticamente más distantes. En el tercer capítulo, para ampliar la estimación de la diversidad genética y las relaciones genéticas entre y dentro de las especies silvestres y cultivadas pertenecientes al complejo berenjena, realizamos un genotipado masivo, mediante un enfoque de genotipado por secuenciación, de 76 accesiones pertenecientes a 17 especies del acervo genético primario, secundario y terciario de la berenjena común. De los 75,399 sitios polimórficos identificados, 12,859 se asociaron a regiones CDS y se usaron para establecer una evaluación exhaustiva y detallada de la diversidad alélica natural y las relaciones genéticas en el acervo genético de la berenjena utilizando tres enfoques diferentes (estructura jerárquica de la población, dendrograma basado en UPGMA y análisis de PCoA). En el cuatro capítulo, desarrollamos un mapa genético interespecífico entre S. incanum y S. melongena, vinculado a otrosFeeding the future burgeoning population in a climate change scenario demands new breeding approaches and tools to develop new resource-efficient and resilient crop varieties. Among vegetable crops, eggplant (Solanum melongena) is recognized as an important food crop and as such is included in the Annex 1 of the International Treaty on Plant Genetic Resources for Food and Agriculture, which includes 34 crops considered as most relevant for mankind. Before the start of this thesis, few genetic and genomic tools and resources for eggplant breeding, which are reviewed in an introductory chapter, were available. We have recognized the importance of wild eggplant relatives, which have been barely used in eggplant breeding. In this respect, in order to make a more efficient use of wild relatives in plant breeding, we proposed an ambitious approach, called "introgressiomics", consisting of a systematic and massive development of materials carrying introgressions from crop wild relatives (CWRs), which usually are an unexplored and unexploited source of genetic variation for breeding traits. The works done in this thesis are related to the application of the introgressiomics approach to eggplant. In this framework, the general objectives of the thesis are the development of genetic and genomic information and tools in eggplant genepool, using a multidisciplinary and multi-pronged approach to assist eggplant breeding in the development of new improved and resilient varieties using eggplant relatives as a source of variation. Specifically, in the first chapter of this thesis, we sequenced the transcriptome of two eggplant related species, the wild Solanum incanum and the cultivated S. aethiopicum, that have a great interest in eggplant breeding. The transcriptomes were assembled in 83,905 and 87,084 unigenes for S. incanum and S. aethiopicum respectively, which were extensively structurally and functionally annotated. The variant call analysis identified tens of thousands intraspecific and interspecific polymorphisms, as well as around a thousand of SSRs in each species. In the second chapter, a subset of those markers (11 SSRs and 35 SNPs) was tested for confirming their usefulness for genetic fingerprinting, diversity evaluation and the establishment of relationships in cultivated eggplant (common, scarlet and gboma) genepools. We observed that SSRs and SNPs provided different results in the establishment of the relationships, suggesting that each marker type sampled different levels of genetic variation. However, although both markers provided a similar level of information, SNPs seem to provide a better resolution than SSRs for materials phylogenetically more distant. In the third chapter, in order to broaden the estimation of the genetic diversity and genetic relationships among and within wild and cultivated species belonging to eggplant complexes, we performed a massive genotyping, by a genotype-by-sequencing approach, of 76 accessions belonging to 17 species from the primary, secondary and tertiary genepool of common eggplant. Out of 75,399 polymorphic sites identified, 12,859 were associated to CDS regions and used to establish an exhaustive and detailed evaluation of the natural allelic diversity and genetic relationships in eggplant genepool using three different approaches (hierarchical population structure, UPGMA-based dendrogram, and PCoA analysis). In the four chapter, we developed an interspecific genetic map between S. incanum and S. melongena, linked to four previous eggplant maps and to one tomato map. A total of 243 molecular markers were successfully mapped consisting of 42 COSII, 99 SSRs, 88 AFLPs, 9 CAPS, 4 SNPs and one morphological polymorphic markers encompassed 1085 cM distributed in 12 linkage groups. Based on the syntheny with tomato, the candidate genes involved in the core chlorogenic acid synthesis pathway in eggplant (PAL, C4H, 4CL, HCT, C3¿H, HQT), five polyphenol oxidase genes (PPO1, PPO2, PPO3, PPAlimentar la futura població en creixement en un context de canvi climàtic exigeix nous enfocaments i eines de millora genètica per desenvolupar noves varietats de cultius que siguin resilients i eficients en l'ús dels recursos. Entre les hortalisses, l'albergínia (Solanum melongena) és reconeguda com un cultiu important i com a tal està inclosa en l'Annex 1 del Tractat Internacional sobre els Recursos Fitogenètics per a l'Alimentació i l'Agricultura, que inclou 34 cultius considerats com els més rellevants per a la humanitat. Abans de l'inici d'aquesta tesi, es disposava de poques eines genètiques i genòmiques per a la millora genètica de l'albergínia, les quals es revisen en un capítol introductori. Així mateix, hem reconegut la importància dels parents silvestres de l'albergínia, que tot just s'han utilitzat en la millora genètica de la mateixa. Referent a això, per fer un ús més eficient dels parents silvestres a la millora genètica, vam proposar un enfocament ambiciós, anomenat "introgressiomics", que consisteix en un desenvolupament sistemàtic i massiu de materials que portin introgresions de parents silvestres (CWR), els quals generalment són una font inexplorada i desaprofitada de variació genètica. Els treballs realitzats en aquesta tesi estan relacionats amb l'aplicació d'aquest enfocament a l'albergínia. En aquest marc, els objectius generals de la tesi són el desenvolupament de la informació i eines genètiques i genòmiques en el patrimoni genètic de l'albergínia, utilitzant un enfocament multidisciplinari i multifacètic per a la millora genètica en el desenvolupament de noves varietats millorades i resistents emprent spècies relacionades com a font de variació. Concretament, en el primer capítol d'aquesta tesi, seqüenciem el transcriptoma de dues espècies relacionades amb l'albergínia, la silvestre Solanum incanum i l'espècie cultivada africana S. aethiopicum, que tenen un gran interès en la millora genètica de l'albergínia. Els transcriptomes s'ensamblaren en 83,905 i 87,084 unigenes per S. incanum i S. aethiopicum respectivament, els quals van ser extensivament anotats estructuralment i funcionalment. La recerca de variants al·lèliques va identificar desenes de milers de polimorfismes intraespecífics i interespecífics, així com al voltant d'un miler de SSRs en cada espècie. En el segon capítol, un subconjunt d'aquests marcadors (11 SSRs i 35 SNPs) es van analitzar per confirmar la seva utilitat per l'empremta genètica, l'avaluació de la diversitat i l'establiment de relacions entre les albergínies conreades (comú, escarlata i gboma). Observem que els SSRs i els SNPs van proporcionar resultats diferents en l'establiment de les relacions, el que suggereix que cada tipus de marcador va mostrejar diferents nivells de variació genètica. No obstant això, encara que tots dos marcadors van proporcionar un nivell similar d'informació, els SNPs semblen proporcionar una millor resolució que els SSRs per materials filogenèticament més distants. En el tercer capítol, per a ampliar l'estimació de la diversitat genètica i les relacions genètiques entre i dins de les espècies silvestres i conreades pertanyents al complex albergínia, vam realitzar un genotipat massiu, mitjançant un enfocament de genotipat per seqüenciació, de 76 accessions pertanyents a 17 espècies del patrimoni genètic primari, secundari i terciari de l'albergínia comuna. Dels 75,399 llocs polimòrfics identificats, 12,859 es van associar a regions CDS i es van usar per a establir una avaluació exhaustiva i detallada de la diversitat al·lèlica natural i les relacions genètiques en el patrimoni genètic de l'albergínia utilitzant tres enfocaments diferents (estructura jeràrquica de la població, dendrograma basat en UPGMA i anàlisi de PCoA). En el quart capítol, desenvolupem un mapa genètic interespecífic entre S. incanum i S. melongena, vinculat a altres quatre mapes anteriorGramazio, P. (2018). GENETICS AND GENOMICS OF CULTIVATED EGGPLANTS AND WILD RELATIVES [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/104605TESISCompendi

Role of Molecular Markers and Importance of SNP for the Development of Cotton Programs

Cotton is an important commercial cash crop and cultivated worldwide. It is very important for improvement of desirable traits for development of cotton crop. In this review paper we have discussed the overall Molecular markers and advance techniques with their utilization in cotton improvement programmers. Molecular markers have reliable results and performance increased research of cotton breeding programs. Molecular markers are used to analyze genomic variations, association mapping, fingerprinting and genetic diversity in cotton crop.SNP markers have many advantages for genotyping of large populations as compared to previous marker systems. It is more advance and efficient processing technique. With the help of SNP technique we get more accurate results as compared to other markers in a short time. Overall DNA markers are used in cotton include Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism, with their history current development, implication and importance in cotton breeding. Keywords PCR Polymerase chain reaction QTLs Quantitative trait loci RAPD Random amplified polymorphic DNA RFLP Restriction fragment length polymorphism RIL Recombinant inbred line SNPs Single nucleotide polymorphisms SSR Simple sequence repea