Journal articles 2015
Documents
Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.)
Keller B, Manzanares C, Jara C, Lobaton JD, Studer B and Raatz B (2015). Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 128(5):813–826 (DOI: 10.1007/s00122-015-2472-6). (G6010.03)
Key message: A major QTL for angular leaf spot resistance in the common bean accession G5686 was fine-mapped to a region containing 36 candidate genes. Markers have been developed for marker-assisted selection.
Abstract: Common bean (Phaseolus vulgaris L.) is an important grain legume and an essential protein source for human nutrition in developing countries. Angular leaf spot (ALS) caused by the pathogen Pseudocercospora griseola (Sacc.) Crous and U. Braun is responsible for severe yield losses of up to 80 %. Breeding for resistant cultivars is the most ecological and economical means to control ALS and is particularly important for yield stability in low-input agriculture. Here, we report on a fine-mapping approach of a major quantitative trait locus (QTL) ALS4.1GS, UC for ALS resistance in a mapping population derived from the resistant genotype G5686 and the susceptible cultivar Sprite. 180 F3 individuals of the mapping population were evaluated for ALS resistance and genotyped with 22 markers distributed over 11 genome regions colocating with previously reported QTL for ALS resistance. Multiple QTL analysis identified three QTL regions, including one major QTL on chromosome Pv04 at 43.7 Mbp explaining over 75 % of the observed variation for ALS resistance. Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes. Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance. Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.
Keller B, Manzanares C, Jara C, Lobaton JD, Studer B and Raatz B (2015). Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 128(5):813–826 (DOI: 10.1007/s00122-015-2472-6). (G6010.03)
Key message: A major QTL for angular leaf spot resistance in the common bean accession G5686 was fine-mapped to a region containing 36 candidate genes. Markers have been developed for marker-assisted selection.
Abstract: Common bean (Phaseolus vulgaris L.) is an important grain legume and an essential protein source for human nutrition in developing countries. Angular leaf spot (ALS) caused by the pathogen Pseudocercospora griseola (Sacc.) Crous and U. Braun is responsible for severe yield losses of up to 80 %. Breeding for resistant cultivars is the most ecological and economical means to control ALS and is particularly important for yield stability in low-input agriculture. Here, we report on a fine-mapping approach of a major quantitative trait locus (QTL) ALS4.1GS, UC for ALS resistance in a mapping population derived from the resistant genotype G5686 and the susceptible cultivar Sprite. 180 F3 individuals of the mapping population were evaluated for ALS resistance and genotyped with 22 markers distributed over 11 genome regions colocating with previously reported QTL for ALS resistance. Multiple QTL analysis identified three QTL regions, including one major QTL on chromosome Pv04 at 43.7 Mbp explaining over 75 % of the observed variation for ALS resistance. Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes. Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance. Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.
Full article
Environmental response and genomic regions correlated with rice root growth and yield under drought in the OryzaSNP panel across multiple study systems
Wade LJ, Bartolome V, Mauleon R, Vasant VD, Prabakar SM, Chelliah M, Kameoka E, Nagendra K, Reddy KRK, Varma CMK, Patil KG, Shrestha R, Al-Shugeairy Z, Al-Ogaidi F, Munasinghe M, Gowda V, Semon M, Suralta RR, Shenoy V, Vadez V, Serraj R, Shashidhar HE, Yamauchi AK, Ranganathan CB, Price A, McNally KL and Henry A (2015). Environmental response and genomic regions correlated with rice root growth and yield under drought in the OryzaSNP panel across multiple study systems. PLoS ONE (DOI: 10.1371/journal.pone.0124127). In press. (G3008.06)
Wade LJ, Bartolome V, Mauleon R, Vasant VD, Prabakar SM, Chelliah M, Kameoka E, Nagendra K, Reddy KRK, Varma CMK, Patil KG, Shrestha R, Al-Shugeairy Z, Al-Ogaidi F, Munasinghe M, Gowda V, Semon M, Suralta RR, Shenoy V, Vadez V, Serraj R, Shashidhar HE, Yamauchi AK, Ranganathan CB, Price A, McNally KL and Henry A (2015). Environmental response and genomic regions correlated with rice root growth and yield under drought in the OryzaSNP panel across multiple study systems. PLoS ONE (DOI: 10.1371/journal.pone.0124127). In press. (G3008.06)
Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses
Pariasca-Tanaka J, Lorieux M, He C, McCouch S, Thomson MJ and Wissuwa M (2015). Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses. Euphytica 201(1):67–78 (DOI: 10.1007/s10681-014-1183-4). First published in June 2014. Not open access; view abstract. (G3005.10)
Pariasca-Tanaka J, Lorieux M, He C, McCouch S, Thomson MJ and Wissuwa M (2015). Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses. Euphytica 201(1):67–78 (DOI: 10.1007/s10681-014-1183-4). First published in June 2014. Not open access; view abstract. (G3005.10)
Development and GBS-genotyping of Introgression Lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga
Arbelaez JD, Moreno LT, Singh N, Tung C-W, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M and McCouch SR (2015). Development and GBS-genotyping of Introgression Lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. Plant Breeding In press. (G3005.10)
Arbelaez JD, Moreno LT, Singh N, Tung C-W, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M and McCouch SR (2015). Development and GBS-genotyping of Introgression Lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. Plant Breeding In press. (G3005.10)
Association of mid-reproductive stage canopy temperature depression with the molecular markers and grain yields of chickpea (Cicer arietinum L.) germplasm under terminal drought
Purushothaman R, Thudi M, Krishnamurthy L, Upadhyaya HD, Kashiwagi J, Gowda CLL and Varshney RK (2015). Association of mid-reproductive stage canopy temperature depression with the molecular markers and grain yields of chickpea (Cicer arietinum L.) germplasm under terminal drought. Field Crops Research 174:1–11 (DOI: 10.1016/j.fcr.2015.01.007). (G4008-12)
Abstract: Canopy temperature depression (CTD) has been used to estimate crop yield and drought tolerance. However, when to measure CTD for the best breeding selection efficacy has seldom been addressed. The objectives of this study were to evaluate CTD as a drought response measure, identify suitable crop stage for measurement and associated molecular markers. CTD was measured using an infrared camera on 59, 62, 69, 73, 76 and 82 days after sowing (DAS) and the grain yield, shoot biomass and harvest index (%). CTD recorded at 62 DAS was positively associated with the grain yield by 40% and shoot biomass by 27% and such association diminished gradually to minimum after 76 DAS. Moreover, CTD at 62 DAS also showed similar positive association with the grain yield recorded in two previous years (r = 0.45***, 0.42***). Genome-wide and candidate gene based association analysis had revealed the presence of nine SSR, 11 DArT and three gene-based markers that varied across the six stages of observation. Two SSR markers were associated with CTD through crop phenology or grain yield while the rest were associated only with CTD for computing marker-trait associations (MTAs). The phenotypic variation explained by the markers was the highest at 62 DAS. These results confirm the importance of continued transpiration and the ability of the roots to supply stored soil water under terminal drought. The selection for grain yield through CTD is done best 15 days after the mean flowering time.
Purushothaman R, Thudi M, Krishnamurthy L, Upadhyaya HD, Kashiwagi J, Gowda CLL and Varshney RK (2015). Association of mid-reproductive stage canopy temperature depression with the molecular markers and grain yields of chickpea (Cicer arietinum L.) germplasm under terminal drought. Field Crops Research 174:1–11 (DOI: 10.1016/j.fcr.2015.01.007). (G4008-12)
Abstract: Canopy temperature depression (CTD) has been used to estimate crop yield and drought tolerance. However, when to measure CTD for the best breeding selection efficacy has seldom been addressed. The objectives of this study were to evaluate CTD as a drought response measure, identify suitable crop stage for measurement and associated molecular markers. CTD was measured using an infrared camera on 59, 62, 69, 73, 76 and 82 days after sowing (DAS) and the grain yield, shoot biomass and harvest index (%). CTD recorded at 62 DAS was positively associated with the grain yield by 40% and shoot biomass by 27% and such association diminished gradually to minimum after 76 DAS. Moreover, CTD at 62 DAS also showed similar positive association with the grain yield recorded in two previous years (r = 0.45***, 0.42***). Genome-wide and candidate gene based association analysis had revealed the presence of nine SSR, 11 DArT and three gene-based markers that varied across the six stages of observation. Two SSR markers were associated with CTD through crop phenology or grain yield while the rest were associated only with CTD for computing marker-trait associations (MTAs). The phenotypic variation explained by the markers was the highest at 62 DAS. These results confirm the importance of continued transpiration and the ability of the roots to supply stored soil water under terminal drought. The selection for grain yield through CTD is done best 15 days after the mean flowering time.
Arachis batizocoi: a study of its relationship to cultivated peanut (A. hypogaea) and its potential for introgression of wild genes into the peanut crop using induced allotetraploids
Leal-Bertioli SCM, Santos SP, Dantas KM, Inglis PW, Nielen S, Araujo ACG, Silva JP, Cavalcante U, Guimarães PM, Brasileiro ACM, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Moretzsohn MC and Bertioli DJ (2015). Arachis batizocoi: a study of its relationship to cultivated peanut (A. hypogaea) and its potential for introgression of wild genes into the peanut crop using induced allotetraploids. Annals of Botany 115(2):237–49 (DOI: 10.1093/aob/mcu237). First published online in December 2014. (G6010.01)
Abstract: Background and Aims Arachis batizocoi is a wild relative of cultivated peanut (A. hypogaea), an allotetraploid with an AABB genome. Arachis batizocoi was once considered the ancestral donor of the peanut B genome, but cytogenetics and DNA phylogenies have indicated a new genome classification, ‘K’. These observations seem inconsistent with genetic studies and breeding that have shown that A. batizocoi can behave as a B genome.
Methods The genetic behaviour, genome composition and phylogenetic position of A. batizocoi were studied using controlled hybridizations, induced tetraploidy, whole-genome in situ fluorescent hybridization (GISH) and molecular phylogenetics.
Key Results Sterile diploid hybrids containing AK genomes were obtained using A. batizocoi and the A genome species A. duranensis, A. stenosperma, A. correntina or A. villosa. From these, three types of AAKK allotetraploids were obtained, each in multiple independent polyploidy events. Induced allotetraploids were vigorous and fertile, and were hybridized to A. hypogaea to produce F1 hybrids. Even with the same parental combination, fertility of these F1 hybrids varied greatly, suggesting the influence of stochastic genetic or epigenetic events. Interestingly, hybrids with A. hypogaea ssp. hypogaea were significantly more fertile than those with the subspecies fastigiata. GISH in cultivated × induced allotetraploids hybrids (harbouring AABK genomes) and a molecular phylogeny using 16 intron sequences showed that the K genome is distinct, but more closely related to the B than to the A genome.
Conclusions The K genome of A. batizocoi is more related to B than to the A genome, but is distinct. As such, when incorporated in an induced allotetraploid (AAKK) it can behave as a B genome in crosses with peanut. However, the fertility of hybrids and their progeny depends upon the compatibility of the A genome interactions. The genetic distinctness of A. batizocoi makes it an important source of allelic diversity in itself, especially in crosses involving A. hypogaea ssp. hypogaea.
Leal-Bertioli SCM, Santos SP, Dantas KM, Inglis PW, Nielen S, Araujo ACG, Silva JP, Cavalcante U, Guimarães PM, Brasileiro ACM, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Moretzsohn MC and Bertioli DJ (2015). Arachis batizocoi: a study of its relationship to cultivated peanut (A. hypogaea) and its potential for introgression of wild genes into the peanut crop using induced allotetraploids. Annals of Botany 115(2):237–49 (DOI: 10.1093/aob/mcu237). First published online in December 2014. (G6010.01)
Abstract: Background and Aims Arachis batizocoi is a wild relative of cultivated peanut (A. hypogaea), an allotetraploid with an AABB genome. Arachis batizocoi was once considered the ancestral donor of the peanut B genome, but cytogenetics and DNA phylogenies have indicated a new genome classification, ‘K’. These observations seem inconsistent with genetic studies and breeding that have shown that A. batizocoi can behave as a B genome.
Methods The genetic behaviour, genome composition and phylogenetic position of A. batizocoi were studied using controlled hybridizations, induced tetraploidy, whole-genome in situ fluorescent hybridization (GISH) and molecular phylogenetics.
Key Results Sterile diploid hybrids containing AK genomes were obtained using A. batizocoi and the A genome species A. duranensis, A. stenosperma, A. correntina or A. villosa. From these, three types of AAKK allotetraploids were obtained, each in multiple independent polyploidy events. Induced allotetraploids were vigorous and fertile, and were hybridized to A. hypogaea to produce F1 hybrids. Even with the same parental combination, fertility of these F1 hybrids varied greatly, suggesting the influence of stochastic genetic or epigenetic events. Interestingly, hybrids with A. hypogaea ssp. hypogaea were significantly more fertile than those with the subspecies fastigiata. GISH in cultivated × induced allotetraploids hybrids (harbouring AABK genomes) and a molecular phylogeny using 16 intron sequences showed that the K genome is distinct, but more closely related to the B than to the A genome.
Conclusions The K genome of A. batizocoi is more related to B than to the A genome, but is distinct. As such, when incorporated in an induced allotetraploid (AAKK) it can behave as a B genome in crosses with peanut. However, the fertility of hybrids and their progeny depends upon the compatibility of the A genome interactions. The genetic distinctness of A. batizocoi makes it an important source of allelic diversity in itself, especially in crosses involving A. hypogaea ssp. hypogaea.
Abiotic stress responses in legumes: Strategies used to cope with environmental challenges
Araújo SS, Beebe S, Crespi M, Delbreil B, González EM, Gruber V, Lejeune-Henaut I, Link W, Monteros MJ, Prats E, Rao I, Vadez V and Vaz Patto MC (2015). Abiotic stress responses in legumes: Strategies used to cope with environmental challenges. Critical Reviews in Plant Sciences 34(1–3):237–280 (DOI: 10.1080/07352689.2014.898450). First published online in October 2014. Not open access; view abstract.
Araújo SS, Beebe S, Crespi M, Delbreil B, González EM, Gruber V, Lejeune-Henaut I, Link W, Monteros MJ, Prats E, Rao I, Vadez V and Vaz Patto MC (2015). Abiotic stress responses in legumes: Strategies used to cope with environmental challenges. Critical Reviews in Plant Sciences 34(1–3):237–280 (DOI: 10.1080/07352689.2014.898450). First published online in October 2014. Not open access; view abstract.
