Procedimiento para identificar y localizar QTLs ; Metodos estadisticos para el mapeo de QTLs ; Po... more Procedimiento para identificar y localizar QTLs ; Metodos estadisticos para el mapeo de QTLs ; Posicion y efecto de un QTL ; Factores que afectan a la identification de un QTL ; Validacion de QTLs ; Genotecas de lineas de introgresion para el aprovechamiento de la variabilidad exotica ; Mapeo fino y clonacion de QTLs ; Superacion de retos y perspectivas futuras
In order to understand the genetic control of quantitative agronomic traits in garden asparagus, ... more In order to understand the genetic control of quantitative agronomic traits in garden asparagus, we performed a quantitative trait loci (QTL) analysis. A population (n = 167) derived from a cross between a female and male plants was evaluated for morpho-agronomic traits over three years. Interval mapping (IM) and restricted multiple QTL mapping (rMQM) analysis was applied, and 18 QTLs were detected. QTLs were located in two linkage groups (LG): 5 in LG5 and 13 in LG6. The physical position of markers of both groups was mapped onto the reference genome through BLAST analysis. LG5 and LG6 match with chromosome 1 (sex-determining chromosome) and chromosome 5, respectively. Haplotypes of both chromosomes of the heterozygous parent and their progeny were obtained, and a bin map was developed. Bins were used to map the QTLs on the reference genome and to perform the association analysis with the morpho-agronomic traits. Two major and stable QTLs over the years (R2 > 10%) for number of ...
Different studies have reported a narrow genetic base for garden asparagus (Asparagus officinalis... more Different studies have reported a narrow genetic base for garden asparagus (Asparagus officinalis L.) due to its common origin, a diploid population (‘Purple Dutch’). The present study focused on the development of new diploid plant material that may be useful to widen the genetic base of the crop by using a tetraploid landrace ‘Morado de Huétor’ (A. officinalis × A. maritimus). With this purpose, a diploid pre-breeding population (n = 1000) carrying introgressions of ‘Morado de Huétor’ has been obtained. This new population derived from crosses under open pollination of a parental collection (n = 77) that was developed in a previous study. The parental collection derived from the first backcrossing using different diploid cultivated plants as a recurrent parent and ‘Morado de Huétor’ as a donor. The genetic diversity of the pre-breeding population was assessed using a set of EST-SSR markers (AG7, AG8, TC1, TC3, TC7, TC9) in a collection of plants (n = 57), which was randomly sample...
Figure S7. Gene structure and transcripts analyses of ARF members in chickpea. The figure shows m... more Figure S7. Gene structure and transcripts analyses of ARF members in chickpea. The figure shows members with genomic truncation (losses of domains III and/or IV), and alternative variants. (PDF 111 kb)
Table S4. Tissue distribution profile of chickpea ARF genes according to the number of expressed ... more Table S4. Tissue distribution profile of chickpea ARF genes according to the number of expressed sequence tags (ESTs) present in NCBI's EST Database. (PNG 886 kb)
Figure S6. Similarity of CaARF genes. Red color shows highest similarity (> 80% identity) foll... more Figure S6. Similarity of CaARF genes. Red color shows highest similarity (> 80% identity) followed by orange (70–80%) and green (60–70%) colors. (PDF 12 kb)
Figure S5. Phylogenetic relationships between the orthologs of CaARF23 in other species. The phyl... more Figure S5. Phylogenetic relationships between the orthologs of CaARF23 in other species. The phylogenetic tree was constructed using the Arabidopsis AtARF2 as an outgroup. The species shown in the figure are Gossypium raimondii (2), Theobroma cacao (1), Citrus clementine (1), Citrus sinensis (1), Populus trichocarpa (2), Vitis vinifera (1), Fragaria vesca (1), Prunus persica (1), Malus domestica (2), Eucalyptus grandis (1), Carica papaya (1), Phaseolus vulgaris (1), Glycine max (2), and Aquilegia coerulea (1). (PDF 55 kb)
Figure S1. geNorm ranking of 4 reference genes from chickpea samples. The expression stability va... more Figure S1. geNorm ranking of 4 reference genes from chickpea samples. The expression stability value (M) is shown as bar plot. Vertical numbers at the top indicate the CV values of the reference genes involved in the normalization. The best pair of references (highly stable expression with M values
Chickpea has considerably increased the genomic resources in recent years providing highly satura... more Chickpea has considerably increased the genomic resources in recent years providing highly saturated genetic maps including anonymous or gene-specific markers targeting some agronomic traits of interest. In addition, the publication of the two draft genome sequences of Kabuli and Desi chickpea types opens a new era in genomic tools. Furthering in our understanding of the association between phenotypic traits (Quantitative Trait loci-QTL-or genes)with the trasncriptome and gene annotation provided by genome sequencing data will be the future challenge to be able to exploit with success marker-assisted Selection (MAS).
A composite linkage map was constructed based on two interspeciWc recombinant inbred line populat... more A composite linkage map was constructed based on two interspeciWc recombinant inbred line populations derived from crosses between Cicer arietinum (ILC72 and ICCL81001) and Cicer reticulatum (Cr5-10 or Cr5-9). These mapping populations segregate for resistance to ascochyta blight (caused by Ascochyta rabiei), fusarium wilt (caused by Fusarium oxysporum f. sp. ciceris) and rust (caused by Uromyces ciceris-arietini). The presence of single nucleotide polymorphisms in ten resistance gene analogs (RGAs) previously isolated and characterized was exploited. Six out of the ten RGAs were novel sequences. In addition, classes RGA05, RGA06, RGA07, RGA08, RGA09 and RGA10 were considerate putatively functional since they matched with several legume expressed sequences tags (ESTs) obtained under infection conditions. Seven RGA PCR-based markers (5 CAPS and 2 dCAPS) were developed and successfully genotyped in the two progenies. Six of them have been mapped in diVerent linkage groups where major quantitative trait loci conferring resistance to ascochyta blight and fusarium wilt have been reported. Genomic locations of RGAs were compared with those of known Cicer R-genes and previously mapped RGAs. Association was detected between RGA05 and genes controlling resistance to fusarium wilt caused by races 0 and 5.
Two quantitative trait loci (QTLs), (QTL(AR1) and QTL(AR2)) associated with resistance to ascochy... more Two quantitative trait loci (QTLs), (QTL(AR1) and QTL(AR2)) associated with resistance to ascochyta blight, caused by Ascochyta rabiei, have been identified in a recombinant inbred line population derived from a cross of kabulixdesi chickpea. The population was evaluated in two cropping seasons under field conditions and the QTLs were found to be located in two different linkage groups (LG4a and LG4b). LG4b was saturated with RAPD markers and four of them associated with resistance were sequenced to give sequence characterized amplified regions (SCARs) that segregated with QTL(AR2). This QTL explained 21% of the total phenotypic variation. However, QTL(AR1), located in LG4a, explained around 34% of the total phenotypic variation in reaction to ascochyta blight when scored in the second cropping season. This LG4a region only includes a few markers, the flower colour locus (B/b), STMS GAA47, a RAPD marker and an inter-simple-sequence-repeat and corresponds with a previously reported QTL. From the four SCARs tagging QTL(AR2), SCAR (SCY17(590)) was co-dominant, and the other three were dominant. All SCARs segregated in a 1:1 (presence:absence) ratio and the scoring co-segregated with their respective RAPD markers. QTL(AR2) on LG4b was mapped in a highly saturated genomic region covering a genetic distance of 0.8 cM with a cluster of nine markers (three SCARs, two sequence-tagged microsatellite sites (STMS) and four RAPDs). Two of the four SCARs showed significant alignment with genes or proteins related to disease resistance in other species and one of them (SCK13(603)) was sited in the highly saturated region linked to QTL(AR2). STMS TA72 and TA146 located in LG4b were described in previous maps where QTL for blight resistance were also localized in both inter and intraspecific crosses. These findings may improve the precision of molecular breeding for QTL(AR2) as they will allow the choice of as much polymorphism as possible in any population and could be the starting point for finding a candidate resistant gene for ascochyta blight resistance in chickpea.
... For breeding purposes this species is frequently divided into two main types: desi and kabuli... more ... For breeding purposes this species is frequently divided into two main types: desi and kabuli,desi having mainly small and coloured seeds and kabuli having large and white ones. ... Desi types are considered as a good source of resistance to Fusarium wilt (Haware et al. ...
A consensus genetic map of chickpea (Cicer arietinum L.) was constructed by merging linkage maps ... more A consensus genetic map of chickpea (Cicer arietinum L.) was constructed by merging linkage maps from 10 different populations, using STMS (Sequence-tagged Microsatellite Sites) as bridging markers. These populations derived from five wide crosses (C. arietinum 9 Cicer reticulatum) and five narrow crosses (Desi 9 Kabuli types) were previously used for mapping genes for several agronomic traits such as ascochyta blight, fusarium wilt, rust resistance, seed weight, flowering time and days to flower. The integrated map obtained from wide crosses consists of 555 loci including, among other markers, 135 STMSs and 33 cross-genome markers distributed on eight linkage groups and covers 652.67 cM. The map obtained from narrow crosses comprises 99 STMSs, 3 SCARs, 1 ASAP, fusarium resistance gene, 5 morphological traits as well as RAPD and ISSR markers distributed on eight linkage groups covering 426.99 cM. Comparison between maps from wide and narrow crosses reflects a general coincidence, Electronic supplementary material The online version of this article (
A chickpea F 2 population of 593 plants derived from the intraspecific cross ILC3279 9 WR315 was ... more A chickpea F 2 population of 593 plants derived from the intraspecific cross ILC3279 9 WR315 was genotyped for markers closely linked to quantitative trait loci (QTLs) for ascochyta blight resistance (QTL AR1 and QTL AR2 located on linkage group 4 and QTL AR3 on linkage group 2). All the markers located on linkage group 4 exhibited strongly distorted segregation with respect to the expected Mendelian inheritance, towards the male parental line. This skewed segregation was also observed in a second F 2 population of 50 plants derived from the same cross, confirming the presence of a region of distorted segregation on this linkage group and its heritability. The most skewed markers were SC-Y17 and TA72, which were tightly linked to each other, indicating that they may both be closely associated with the genetic factor responsible for segregation distortion in chickpea. To attempt to explain the non-Mendelian segregation, by identifying factors to which it could be attributed, three different chisquare tests were carried out to test different hypotheses using the data obtained from examining co-dominant markers associated with segregation distortion. According to our results, the distorted segregation could be caused by gametophytic factors that affect either male or female gametes. Pollen fertility and meiosis were also analysed to determine their relationship with segregation distortion; however, these not seem to be inducing factors in the non-Mendelian segregation reported in this study.
Quantitative traits, seed size, yield and days to flowering were studied in a chickpea intraspeci... more Quantitative traits, seed size, yield and days to flowering were studied in a chickpea intraspecific recombinant inbred line (RIL) population (F6:7) derived from a Kabuli × Desi cross. The population was evaluated in two locations over 2 years. Days to flowering was also evaluated in the greenhouse under short‐day conditions. Seed size was the most heritable trait (0.90), followed by days to flowering (0.36) and yield (0.14). Negative and significant correlation was found between yield and seed size in the second year where environmental homogeneity was tested by analysing the controls included in each assay. During the first year, the environment was not considered homogeneous for yield in either location. Quantitative trait loci (QTLs) for the three characters were detected in linkage group (LG) 4. In relation to seed size, two QTLs were located in LG4 (QTLSW1) and LG8 (QTLSW2). QTLSW1 accounted 20.3% of the total phenotypic variation and QTLSW2 explained 10.1%. A QTL for yield (Q...
Procedimiento para identificar y localizar QTLs ; Metodos estadisticos para el mapeo de QTLs ; Po... more Procedimiento para identificar y localizar QTLs ; Metodos estadisticos para el mapeo de QTLs ; Posicion y efecto de un QTL ; Factores que afectan a la identification de un QTL ; Validacion de QTLs ; Genotecas de lineas de introgresion para el aprovechamiento de la variabilidad exotica ; Mapeo fino y clonacion de QTLs ; Superacion de retos y perspectivas futuras
In order to understand the genetic control of quantitative agronomic traits in garden asparagus, ... more In order to understand the genetic control of quantitative agronomic traits in garden asparagus, we performed a quantitative trait loci (QTL) analysis. A population (n = 167) derived from a cross between a female and male plants was evaluated for morpho-agronomic traits over three years. Interval mapping (IM) and restricted multiple QTL mapping (rMQM) analysis was applied, and 18 QTLs were detected. QTLs were located in two linkage groups (LG): 5 in LG5 and 13 in LG6. The physical position of markers of both groups was mapped onto the reference genome through BLAST analysis. LG5 and LG6 match with chromosome 1 (sex-determining chromosome) and chromosome 5, respectively. Haplotypes of both chromosomes of the heterozygous parent and their progeny were obtained, and a bin map was developed. Bins were used to map the QTLs on the reference genome and to perform the association analysis with the morpho-agronomic traits. Two major and stable QTLs over the years (R2 > 10%) for number of ...
Different studies have reported a narrow genetic base for garden asparagus (Asparagus officinalis... more Different studies have reported a narrow genetic base for garden asparagus (Asparagus officinalis L.) due to its common origin, a diploid population (‘Purple Dutch’). The present study focused on the development of new diploid plant material that may be useful to widen the genetic base of the crop by using a tetraploid landrace ‘Morado de Huétor’ (A. officinalis × A. maritimus). With this purpose, a diploid pre-breeding population (n = 1000) carrying introgressions of ‘Morado de Huétor’ has been obtained. This new population derived from crosses under open pollination of a parental collection (n = 77) that was developed in a previous study. The parental collection derived from the first backcrossing using different diploid cultivated plants as a recurrent parent and ‘Morado de Huétor’ as a donor. The genetic diversity of the pre-breeding population was assessed using a set of EST-SSR markers (AG7, AG8, TC1, TC3, TC7, TC9) in a collection of plants (n = 57), which was randomly sample...
Figure S7. Gene structure and transcripts analyses of ARF members in chickpea. The figure shows m... more Figure S7. Gene structure and transcripts analyses of ARF members in chickpea. The figure shows members with genomic truncation (losses of domains III and/or IV), and alternative variants. (PDF 111 kb)
Table S4. Tissue distribution profile of chickpea ARF genes according to the number of expressed ... more Table S4. Tissue distribution profile of chickpea ARF genes according to the number of expressed sequence tags (ESTs) present in NCBI's EST Database. (PNG 886 kb)
Figure S6. Similarity of CaARF genes. Red color shows highest similarity (> 80% identity) foll... more Figure S6. Similarity of CaARF genes. Red color shows highest similarity (> 80% identity) followed by orange (70–80%) and green (60–70%) colors. (PDF 12 kb)
Figure S5. Phylogenetic relationships between the orthologs of CaARF23 in other species. The phyl... more Figure S5. Phylogenetic relationships between the orthologs of CaARF23 in other species. The phylogenetic tree was constructed using the Arabidopsis AtARF2 as an outgroup. The species shown in the figure are Gossypium raimondii (2), Theobroma cacao (1), Citrus clementine (1), Citrus sinensis (1), Populus trichocarpa (2), Vitis vinifera (1), Fragaria vesca (1), Prunus persica (1), Malus domestica (2), Eucalyptus grandis (1), Carica papaya (1), Phaseolus vulgaris (1), Glycine max (2), and Aquilegia coerulea (1). (PDF 55 kb)
Figure S1. geNorm ranking of 4 reference genes from chickpea samples. The expression stability va... more Figure S1. geNorm ranking of 4 reference genes from chickpea samples. The expression stability value (M) is shown as bar plot. Vertical numbers at the top indicate the CV values of the reference genes involved in the normalization. The best pair of references (highly stable expression with M values
Chickpea has considerably increased the genomic resources in recent years providing highly satura... more Chickpea has considerably increased the genomic resources in recent years providing highly saturated genetic maps including anonymous or gene-specific markers targeting some agronomic traits of interest. In addition, the publication of the two draft genome sequences of Kabuli and Desi chickpea types opens a new era in genomic tools. Furthering in our understanding of the association between phenotypic traits (Quantitative Trait loci-QTL-or genes)with the trasncriptome and gene annotation provided by genome sequencing data will be the future challenge to be able to exploit with success marker-assisted Selection (MAS).
A composite linkage map was constructed based on two interspeciWc recombinant inbred line populat... more A composite linkage map was constructed based on two interspeciWc recombinant inbred line populations derived from crosses between Cicer arietinum (ILC72 and ICCL81001) and Cicer reticulatum (Cr5-10 or Cr5-9). These mapping populations segregate for resistance to ascochyta blight (caused by Ascochyta rabiei), fusarium wilt (caused by Fusarium oxysporum f. sp. ciceris) and rust (caused by Uromyces ciceris-arietini). The presence of single nucleotide polymorphisms in ten resistance gene analogs (RGAs) previously isolated and characterized was exploited. Six out of the ten RGAs were novel sequences. In addition, classes RGA05, RGA06, RGA07, RGA08, RGA09 and RGA10 were considerate putatively functional since they matched with several legume expressed sequences tags (ESTs) obtained under infection conditions. Seven RGA PCR-based markers (5 CAPS and 2 dCAPS) were developed and successfully genotyped in the two progenies. Six of them have been mapped in diVerent linkage groups where major quantitative trait loci conferring resistance to ascochyta blight and fusarium wilt have been reported. Genomic locations of RGAs were compared with those of known Cicer R-genes and previously mapped RGAs. Association was detected between RGA05 and genes controlling resistance to fusarium wilt caused by races 0 and 5.
Two quantitative trait loci (QTLs), (QTL(AR1) and QTL(AR2)) associated with resistance to ascochy... more Two quantitative trait loci (QTLs), (QTL(AR1) and QTL(AR2)) associated with resistance to ascochyta blight, caused by Ascochyta rabiei, have been identified in a recombinant inbred line population derived from a cross of kabulixdesi chickpea. The population was evaluated in two cropping seasons under field conditions and the QTLs were found to be located in two different linkage groups (LG4a and LG4b). LG4b was saturated with RAPD markers and four of them associated with resistance were sequenced to give sequence characterized amplified regions (SCARs) that segregated with QTL(AR2). This QTL explained 21% of the total phenotypic variation. However, QTL(AR1), located in LG4a, explained around 34% of the total phenotypic variation in reaction to ascochyta blight when scored in the second cropping season. This LG4a region only includes a few markers, the flower colour locus (B/b), STMS GAA47, a RAPD marker and an inter-simple-sequence-repeat and corresponds with a previously reported QTL. From the four SCARs tagging QTL(AR2), SCAR (SCY17(590)) was co-dominant, and the other three were dominant. All SCARs segregated in a 1:1 (presence:absence) ratio and the scoring co-segregated with their respective RAPD markers. QTL(AR2) on LG4b was mapped in a highly saturated genomic region covering a genetic distance of 0.8 cM with a cluster of nine markers (three SCARs, two sequence-tagged microsatellite sites (STMS) and four RAPDs). Two of the four SCARs showed significant alignment with genes or proteins related to disease resistance in other species and one of them (SCK13(603)) was sited in the highly saturated region linked to QTL(AR2). STMS TA72 and TA146 located in LG4b were described in previous maps where QTL for blight resistance were also localized in both inter and intraspecific crosses. These findings may improve the precision of molecular breeding for QTL(AR2) as they will allow the choice of as much polymorphism as possible in any population and could be the starting point for finding a candidate resistant gene for ascochyta blight resistance in chickpea.
... For breeding purposes this species is frequently divided into two main types: desi and kabuli... more ... For breeding purposes this species is frequently divided into two main types: desi and kabuli,desi having mainly small and coloured seeds and kabuli having large and white ones. ... Desi types are considered as a good source of resistance to Fusarium wilt (Haware et al. ...
A consensus genetic map of chickpea (Cicer arietinum L.) was constructed by merging linkage maps ... more A consensus genetic map of chickpea (Cicer arietinum L.) was constructed by merging linkage maps from 10 different populations, using STMS (Sequence-tagged Microsatellite Sites) as bridging markers. These populations derived from five wide crosses (C. arietinum 9 Cicer reticulatum) and five narrow crosses (Desi 9 Kabuli types) were previously used for mapping genes for several agronomic traits such as ascochyta blight, fusarium wilt, rust resistance, seed weight, flowering time and days to flower. The integrated map obtained from wide crosses consists of 555 loci including, among other markers, 135 STMSs and 33 cross-genome markers distributed on eight linkage groups and covers 652.67 cM. The map obtained from narrow crosses comprises 99 STMSs, 3 SCARs, 1 ASAP, fusarium resistance gene, 5 morphological traits as well as RAPD and ISSR markers distributed on eight linkage groups covering 426.99 cM. Comparison between maps from wide and narrow crosses reflects a general coincidence, Electronic supplementary material The online version of this article (
A chickpea F 2 population of 593 plants derived from the intraspecific cross ILC3279 9 WR315 was ... more A chickpea F 2 population of 593 plants derived from the intraspecific cross ILC3279 9 WR315 was genotyped for markers closely linked to quantitative trait loci (QTLs) for ascochyta blight resistance (QTL AR1 and QTL AR2 located on linkage group 4 and QTL AR3 on linkage group 2). All the markers located on linkage group 4 exhibited strongly distorted segregation with respect to the expected Mendelian inheritance, towards the male parental line. This skewed segregation was also observed in a second F 2 population of 50 plants derived from the same cross, confirming the presence of a region of distorted segregation on this linkage group and its heritability. The most skewed markers were SC-Y17 and TA72, which were tightly linked to each other, indicating that they may both be closely associated with the genetic factor responsible for segregation distortion in chickpea. To attempt to explain the non-Mendelian segregation, by identifying factors to which it could be attributed, three different chisquare tests were carried out to test different hypotheses using the data obtained from examining co-dominant markers associated with segregation distortion. According to our results, the distorted segregation could be caused by gametophytic factors that affect either male or female gametes. Pollen fertility and meiosis were also analysed to determine their relationship with segregation distortion; however, these not seem to be inducing factors in the non-Mendelian segregation reported in this study.
Quantitative traits, seed size, yield and days to flowering were studied in a chickpea intraspeci... more Quantitative traits, seed size, yield and days to flowering were studied in a chickpea intraspecific recombinant inbred line (RIL) population (F6:7) derived from a Kabuli × Desi cross. The population was evaluated in two locations over 2 years. Days to flowering was also evaluated in the greenhouse under short‐day conditions. Seed size was the most heritable trait (0.90), followed by days to flowering (0.36) and yield (0.14). Negative and significant correlation was found between yield and seed size in the second year where environmental homogeneity was tested by analysing the controls included in each assay. During the first year, the environment was not considered homogeneous for yield in either location. Quantitative trait loci (QTLs) for the three characters were detected in linkage group (LG) 4. In relation to seed size, two QTLs were located in LG4 (QTLSW1) and LG8 (QTLSW2). QTLSW1 accounted 20.3% of the total phenotypic variation and QTLSW2 explained 10.1%. A QTL for yield (Q...
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