Journal articles 2014
Documents
The use of SNP markers for linkage mapping in diploid and tetraploid peanuts
Bertioli DJ, Ozias-Akins P, Chu Y, Dantas KM, Santos SP, Gouvea E, Guimarães PM, Leal-Bertioli SCM, Knapp SJ and Moretzsohn MC (2014). The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3 4(1):89–96. First published online in November 2013. (G6010.01)
Abstract: Single nucleotide polymorphic markers (SNPs) are attractive for use in genetic mapping and marker-assisted breeding because they can be scored in parallel assays at favorable costs. However, scoring SNP markers in polyploid plants like the peanut is problematic because of interfering signal generated from the DNA bases that are homeologous to those being assayed. The present study used a previously constructed 1536 GoldenGate SNP assay developed using SNPs identified between two A. duranensis accessions. In this study, the performance of this assay was tested on two RIL mapping populations, one diploid (A. duranensis × A. stenosperma) and one tetraploid [A. hypogaea cv. Runner IAC 886 × synthetic tetraploid (A. ipaënsis × A. duranensis)4×]. The scoring was performed using the software GenomeStudio version 2011.1. For the diploid, polymorphic markers provided excellent genotyping scores with default software parameters. In the tetraploid, as expected, most of the polymorphic markers provided signal intensity plots that were distorted compared to diploid patterns and that were incorrectly scored using default parameters. However, these scorings were easily corrected using the GenomeStudio software. The degree of distortion was highly variable. Of the polymorphic markers, approximately 10% showed no distortion at all behaving as expected for single-dose markers, and another 30% showed low distortion and could be considered high-quality. The genotyped markers were incorporated into diploid and tetraploid genetic maps of Arachis and, in the latter case, were located almost entirely on A genome linkage groups.
Bertioli DJ, Ozias-Akins P, Chu Y, Dantas KM, Santos SP, Gouvea E, Guimarães PM, Leal-Bertioli SCM, Knapp SJ and Moretzsohn MC (2014). The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3 4(1):89–96. First published online in November 2013. (G6010.01)
Abstract: Single nucleotide polymorphic markers (SNPs) are attractive for use in genetic mapping and marker-assisted breeding because they can be scored in parallel assays at favorable costs. However, scoring SNP markers in polyploid plants like the peanut is problematic because of interfering signal generated from the DNA bases that are homeologous to those being assayed. The present study used a previously constructed 1536 GoldenGate SNP assay developed using SNPs identified between two A. duranensis accessions. In this study, the performance of this assay was tested on two RIL mapping populations, one diploid (A. duranensis × A. stenosperma) and one tetraploid [A. hypogaea cv. Runner IAC 886 × synthetic tetraploid (A. ipaënsis × A. duranensis)4×]. The scoring was performed using the software GenomeStudio version 2011.1. For the diploid, polymorphic markers provided excellent genotyping scores with default software parameters. In the tetraploid, as expected, most of the polymorphic markers provided signal intensity plots that were distorted compared to diploid patterns and that were incorrectly scored using default parameters. However, these scorings were easily corrected using the GenomeStudio software. The degree of distortion was highly variable. Of the polymorphic markers, approximately 10% showed no distortion at all behaving as expected for single-dose markers, and another 30% showed low distortion and could be considered high-quality. The genotyped markers were incorporated into diploid and tetraploid genetic maps of Arachis and, in the latter case, were located almost entirely on A genome linkage groups.
Full article
Bulk genetic characterization of Ghanaian maize landraces using microsatellite markers
Oppong A, Bedoya CA, Ewool MB, Asante MD, Thompson RN, Adu-Dapaah H, Lamptey JNL, Ofori K, Offei SK and Warburton ML (2014). Bulk genetic characterization of Ghanaian maize landraces using microsatellite markers. Maydica 59:1–8. (G4007.13.04)
Abstract: Maize (Zea mays L) was first introduced into Ghana over five centuries ago and remains the most important cereal staple, grown in all agro-ecologies across the country. Yield from farmers' fields are low, which is attributed in part to farmer's preferences and/or reliance on local landraces for cultivation. Efforts are underway to improve some of these landraces for improved productivity. Seeds of maize landraces cultivated in all agro-ecologies were collected for genetic characterization using a bulked fingerprinting technique and 20 SSR markers. In all, 20 populations of 15 plants each from Ghana and 4 control populations from Latin America were characterized. The cluster analysis grouped the 20 landraces into two major groups corresponding to the vegetation/climatic conditions of the north and south of the country. Genotypes from Ashanti, which is centrally located, fell into both major clusters, which suggest its importance in maize seed distribution in Ghana and also the diverse climate/vegetation. Structure analyses grouped the genotypes into two major clusters similar to the UPGMA cluster, and populations were not fully distinct according to F statistics. The results suggest that breeders should make performance data available to seed dealers for better productivity.
Oppong A, Bedoya CA, Ewool MB, Asante MD, Thompson RN, Adu-Dapaah H, Lamptey JNL, Ofori K, Offei SK and Warburton ML (2014). Bulk genetic characterization of Ghanaian maize landraces using microsatellite markers. Maydica 59:1–8. (G4007.13.04)
Abstract: Maize (Zea mays L) was first introduced into Ghana over five centuries ago and remains the most important cereal staple, grown in all agro-ecologies across the country. Yield from farmers' fields are low, which is attributed in part to farmer's preferences and/or reliance on local landraces for cultivation. Efforts are underway to improve some of these landraces for improved productivity. Seeds of maize landraces cultivated in all agro-ecologies were collected for genetic characterization using a bulked fingerprinting technique and 20 SSR markers. In all, 20 populations of 15 plants each from Ghana and 4 control populations from Latin America were characterized. The cluster analysis grouped the 20 landraces into two major groups corresponding to the vegetation/climatic conditions of the north and south of the country. Genotypes from Ashanti, which is centrally located, fell into both major clusters, which suggest its importance in maize seed distribution in Ghana and also the diverse climate/vegetation. Structure analyses grouped the genotypes into two major clusters similar to the UPGMA cluster, and populations were not fully distinct according to F statistics. The results suggest that breeders should make performance data available to seed dealers for better productivity.
Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB
Caniato FF, Hamblin MT, Guimaraes CT, Zhang Z, Schaffert RE, Kochian LV and Magalhaes JV (2014). Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB. PLoS ONE 9(1):e87438 (DOI: 10.1371/journal.pone.0087438).
Abstract: Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ~6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity.
Caniato FF, Hamblin MT, Guimaraes CT, Zhang Z, Schaffert RE, Kochian LV and Magalhaes JV (2014). Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB. PLoS ONE 9(1):e87438 (DOI: 10.1371/journal.pone.0087438).
Abstract: Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ~6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity.
Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.)
Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A, Jukanti AK, Jayalakshmi V, Vemula A, Singh SJ, Yasin M, Sheshshayee MS and Viswanatha KP (2014). Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 127(2):445–462 (DOI: 10.1007/s00122-013-2230-6). First published online in December 2013.
Key message: Analysis of phenotypic data for 20 drought tolerance traits in 1–7 seasons at 1–5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement.
Abstract: Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50 % production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations—ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1–7 seasons at 1–5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed (http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20 % phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19 % phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48 % robust M-QTLs for 12 traits and explaining about 58.20 % phenotypic variation present on CaLG04 has been referred as “QTL-hotspot”. This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea.
Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A, Jukanti AK, Jayalakshmi V, Vemula A, Singh SJ, Yasin M, Sheshshayee MS and Viswanatha KP (2014). Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 127(2):445–462 (DOI: 10.1007/s00122-013-2230-6). First published online in December 2013.
Key message: Analysis of phenotypic data for 20 drought tolerance traits in 1–7 seasons at 1–5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement.
Abstract: Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50 % production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations—ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1–7 seasons at 1–5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed (http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20 % phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19 % phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48 % robust M-QTLs for 12 traits and explaining about 58.20 % phenotypic variation present on CaLG04 has been referred as “QTL-hotspot”. This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea.
Genotypic performance under intermittent and terminal drought screening in rainfed lowland rice
Xangsayasane P, Jongdee B, Pantuwan G., Fukai S, Mitchell JH, Inthapanya P and Jothityangkoon D (2014). Genotypic performance under intermittent and terminal drought screening in rainfed lowland rice. Field Crops Research 156:281–292 (DOI: 10.1016/j.fcr.2013.10.017). Not open access; view abstract. (G3008.06)
Xangsayasane P, Jongdee B, Pantuwan G., Fukai S, Mitchell JH, Inthapanya P and Jothityangkoon D (2014). Genotypic performance under intermittent and terminal drought screening in rainfed lowland rice. Field Crops Research 156:281–292 (DOI: 10.1016/j.fcr.2013.10.017). Not open access; view abstract. (G3008.06)
Although drought intensity increases aflatoxin contamination, drought tolerance does not lead to less aflatoxin contamination
Hamidou F, Rathore A, Waliyar F and Vadez V (2014). Although drought intensity increases aflatoxin contamination, drought tolerance does not lead to less aflatoxin contamination. Field Crops Research 156:103–110 (DOI: 10.1016/j.fcr.2013.10.019).
Highlights:
- Groundnut germplasm was assessed across varying drought intensities.
- Drought intensity increased aflatoxin concentration in seeds.
- Across trials aflatoxin concentration and grain yield reduction were highly correlated.
- However within trial, aflatoxin and grain yield reduction were unrelated, showing no direct relationship between drought tolerance and resistance to aflatoxin contamination.
- Mechanisms of drought tolerance and aflatoxin contamination are likely not common.
Abstract: Drought stress is known to increase aflatoxin contamination in groundnut and establishing a possible relationship between drought tolerance and resistance to aflatoxin contamination could contribute to a more efficient selection of aflatoxin-resistant genotypes. In recent work, the reference collection of groundnut had been assessed across seasons varying for drought intensity, i.e. two moderate temperature (rainy season) and two high temperature (dry season) experiments under well-watered (WW) and water stress (WS) conditions (Hamidou et al., 2012 and Hamidou et al., 2013). Here aflatoxin concentration (AC) in seeds is measured in these trials, first for possibly identifying germplasm with low aflatoxin concentrations and second for investigating possible relationships between aflatoxin concentration and drought tolerance. Drought stress intensity increased aflatoxin concentration in seeds and higher aflatoxin contamination was observed under combined drought and high temperature conditions than under drought alone. No germplasm with lower AC than resistant check (55-437) were found. Aflatoxin contamination showed very high GxE interactions, which suggest that selection for resistance to aflatoxin contamination must be specific to environment. Across trials, using means for each environment, there was a clear positive relationship between the aflatoxin concentration and the grain yield reduction due to drought, indicating that a higher drought severity led to higher aflatoxin concentration. However, within trial, the same relationships applied to individual genotypes, or to cohorts of tolerant/sensitive genotypes, were not significant. The major conclusion of this work is that while drought intensity did increase the level of aflatoxin contamination, as expected and previously reported, there seemed to be no direct relationship between tolerance to drought and aflatoxin concentration, suggesting that the mechanisms of drought tolerance and aflatoxin contamination are likely not common.
Hamidou F, Rathore A, Waliyar F and Vadez V (2014). Although drought intensity increases aflatoxin contamination, drought tolerance does not lead to less aflatoxin contamination. Field Crops Research 156:103–110 (DOI: 10.1016/j.fcr.2013.10.019).
Highlights:
- Groundnut germplasm was assessed across varying drought intensities.
- Drought intensity increased aflatoxin concentration in seeds.
- Across trials aflatoxin concentration and grain yield reduction were highly correlated.
- However within trial, aflatoxin and grain yield reduction were unrelated, showing no direct relationship between drought tolerance and resistance to aflatoxin contamination.
- Mechanisms of drought tolerance and aflatoxin contamination are likely not common.
Abstract: Drought stress is known to increase aflatoxin contamination in groundnut and establishing a possible relationship between drought tolerance and resistance to aflatoxin contamination could contribute to a more efficient selection of aflatoxin-resistant genotypes. In recent work, the reference collection of groundnut had been assessed across seasons varying for drought intensity, i.e. two moderate temperature (rainy season) and two high temperature (dry season) experiments under well-watered (WW) and water stress (WS) conditions (Hamidou et al., 2012 and Hamidou et al., 2013). Here aflatoxin concentration (AC) in seeds is measured in these trials, first for possibly identifying germplasm with low aflatoxin concentrations and second for investigating possible relationships between aflatoxin concentration and drought tolerance. Drought stress intensity increased aflatoxin concentration in seeds and higher aflatoxin contamination was observed under combined drought and high temperature conditions than under drought alone. No germplasm with lower AC than resistant check (55-437) were found. Aflatoxin contamination showed very high GxE interactions, which suggest that selection for resistance to aflatoxin contamination must be specific to environment. Across trials, using means for each environment, there was a clear positive relationship between the aflatoxin concentration and the grain yield reduction due to drought, indicating that a higher drought severity led to higher aflatoxin concentration. However, within trial, the same relationships applied to individual genotypes, or to cohorts of tolerant/sensitive genotypes, were not significant. The major conclusion of this work is that while drought intensity did increase the level of aflatoxin contamination, as expected and previously reported, there seemed to be no direct relationship between tolerance to drought and aflatoxin concentration, suggesting that the mechanisms of drought tolerance and aflatoxin contamination are likely not common.
N- and P- mediated seminal root elongation response in rice seedlings
Ogawa S, Gomez Selvaraj M, Joseph Fernando A, Lorieux M, Ishitani M, McCouch S and Arbelaez JD (2014). N- and P- mediated seminal root elongation response in rice seedlings. Plant and Soil 375(1-2):303–315 (DOI: 10.1007/s11104-013-1955-y). First published in November 2013. Not open access; view abstract. (G3005.10)
Ogawa S, Gomez Selvaraj M, Joseph Fernando A, Lorieux M, Ishitani M, McCouch S and Arbelaez JD (2014). N- and P- mediated seminal root elongation response in rice seedlings. Plant and Soil 375(1-2):303–315 (DOI: 10.1007/s11104-013-1955-y). First published in November 2013. Not open access; view abstract. (G3005.10)
Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan
Guimaraes CT, Simoes CC, Pastina MM, Maron LG, Magalhaes JV, Vasconcellos RCC, Guimaraes LJM, Lana UGP, Tinoco CFS, Noda RW, Jardim-Belicuas SN, Kochian LV, Alves VMC and Parentoni SN (2014). Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan. BMC Genomics 15:153 (DOI: 10.1186/1471-2164-15-153). (G7010.03.02)
Abstract: Background Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.
Results Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al3+ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.
Conclusions High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.
Guimaraes CT, Simoes CC, Pastina MM, Maron LG, Magalhaes JV, Vasconcellos RCC, Guimaraes LJM, Lana UGP, Tinoco CFS, Noda RW, Jardim-Belicuas SN, Kochian LV, Alves VMC and Parentoni SN (2014). Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan. BMC Genomics 15:153 (DOI: 10.1186/1471-2164-15-153). (G7010.03.02)
Abstract: Background Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.
Results Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al3+ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.
Conclusions High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.
Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O and Luo MC (2014). Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Functional & Integrative Genomics 14(1): 59–73 (DOI: 10.1007/s10142-014-0363-6).
Abstract: Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O and Luo MC (2014). Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Functional & Integrative Genomics 14(1): 59–73 (DOI: 10.1007/s10142-014-0363-6).
Abstract: Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
Marker-assisted backcrossing to introgress resistance to fusarium wilt race 1 and ascochyta blight in C 214, an elite cultivar of chickpea
Varshney RK, Mohan SM, Gaur PM, Chamarthi SK, Singh VK, Srinivasan S, Swapna N, Sharma M, Pande S, Singh S, Kaur L (2014). Marker-assisted backcrossing to introgress resistance to fusarium wilt race 1 and ascochyta blight in C 214, an elite cultivar of chickpea. The Plant Genome 7(1) (DOI: 10.3835/plantgenome2013.10.0035).
Abstract: Fusarium wilt (FW) and Ascochyta blight (AB) are two major constraints to chickpea (Cicer arietinum ) production,Fusarium wilt (FW) and Ascochyta blight (AB) are two major constraints to chickpea (Cicer arietinum L.) production. Therefore, two parallel marker-assisted backcrossing (MABC) programs by targeting foc1 locus and two quantitative trait loci (QTL) regions, ABQTL-I and ABQTL-II, were undertaken to introgress resistance to FW and AB, respectively, in C 214, an elite cultivar of chickpea. In the case of FW, foreground selection (FGS) was conducted with six markers (TR19, TA194, TAA60, GA16, TA110, and TS82) linked to foc1 in the cross C 214 × WR 315 (FW-resistant). On the other hand, eight markers (TA194, TR58, TS82, GA16, SCY17, TA130, TA2, and GAA47) linked with ABQTL-I and ABQTL-II were used in the case of AB by deploying C 214 × ILC 3279 (AB-resistant) cross.
Varshney RK, Mohan SM, Gaur PM, Chamarthi SK, Singh VK, Srinivasan S, Swapna N, Sharma M, Pande S, Singh S, Kaur L (2014). Marker-assisted backcrossing to introgress resistance to fusarium wilt race 1 and ascochyta blight in C 214, an elite cultivar of chickpea. The Plant Genome 7(1) (DOI: 10.3835/plantgenome2013.10.0035).
Abstract: Fusarium wilt (FW) and Ascochyta blight (AB) are two major constraints to chickpea (Cicer arietinum ) production,Fusarium wilt (FW) and Ascochyta blight (AB) are two major constraints to chickpea (Cicer arietinum L.) production. Therefore, two parallel marker-assisted backcrossing (MABC) programs by targeting foc1 locus and two quantitative trait loci (QTL) regions, ABQTL-I and ABQTL-II, were undertaken to introgress resistance to FW and AB, respectively, in C 214, an elite cultivar of chickpea. In the case of FW, foreground selection (FGS) was conducted with six markers (TR19, TA194, TAA60, GA16, TA110, and TS82) linked to foc1 in the cross C 214 × WR 315 (FW-resistant). On the other hand, eight markers (TA194, TR58, TS82, GA16, SCY17, TA130, TA2, and GAA47) linked with ABQTL-I and ABQTL-II were used in the case of AB by deploying C 214 × ILC 3279 (AB-resistant) cross.
