Journal articles 2015
Documents
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)
QTL mapping for plant height and yield components in common wheat under water limited and full irrigation environments
Li X, Xia X, Xiao Y, He Z, Wang D, Trethowan R, Wang H, Chen X (2015). QTL mapping for plant height and yield components in common wheat under water limited and full irrigation environments. Crop & Pasture Science Accepted for publication. View abstract. (G7010.02.01)
Li X, Xia X, Xiao Y, He Z, Wang D, Trethowan R, Wang H, Chen X (2015). QTL mapping for plant height and yield components in common wheat under water limited and full irrigation environments. Crop & Pasture Science Accepted for publication. View abstract. (G7010.02.01)
Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought
Henry A, Swamy BPM, Dixit S, Torres RD, Batoto TC, Manalili M, Anantha MS, Mandal NP and Kumar A (2015). Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought. Journal of Experimental Botany 66(7):1787–1799 (DOI: 10.1093/jxb/eru506). (G3008.06)
Abstract: Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs—as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY2.2 + qDTY4.1) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY2.2 and qDTY4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.
Henry A, Swamy BPM, Dixit S, Torres RD, Batoto TC, Manalili M, Anantha MS, Mandal NP and Kumar A (2015). Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought. Journal of Experimental Botany 66(7):1787–1799 (DOI: 10.1093/jxb/eru506). (G3008.06)
Abstract: Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs—as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY2.2 + qDTY4.1) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY2.2 and qDTY4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.
Full article
Genetic variation in lowland sorghum (Sorghum bicolor (L.) Moench) landraces assessed by simple sequence repeats
Amelework B, Shimelis H, Tongoona P, Laing M and Mengistu F (2015). Genetic variation in lowland sorghum (Sorghum bicolor (L.) Moench) landraces assessed by simple sequence repeats. Plant Genetic Resources Published online: 26 June 2014 (DOI: 10.1017/S1479262114000744). Not open access; view abstract.
Amelework B, Shimelis H, Tongoona P, Laing M and Mengistu F (2015). Genetic variation in lowland sorghum (Sorghum bicolor (L.) Moench) landraces assessed by simple sequence repeats. Plant Genetic Resources Published online: 26 June 2014 (DOI: 10.1017/S1479262114000744). Not open access; view abstract.
Genetic purity and patterns of relationships among tropical highland adapted quality protein and normal maize inbred lines using microsatellite markers
Abakemal D, Shimelis H, Derera J and Semagn K (2015). Genetic purity and patterns of relationships among tropical highland adapted quality protein and normal maize inbred lines using microsatellite markers. Euphytica Published online: 23 December 2014 (DOI 10.1007/s10681-014-1332-9). Not open access; view abstract.
Abakemal D, Shimelis H, Derera J and Semagn K (2015). Genetic purity and patterns of relationships among tropical highland adapted quality protein and normal maize inbred lines using microsatellite markers. Euphytica Published online: 23 December 2014 (DOI 10.1007/s10681-014-1332-9). Not open access; view abstract.
Quantitative trait loci mapping for traits related to the progression of wheat flag leaf senescence
Wang S, Liang Z, Sun D, Dong F, Chen W, Wang H and Jing R (2015). Quantitative trait loci mapping for traits related to the progression of wheat flag leaf senescence. Journal of Agricultural Science Published online as FirstView Article: 24 September 2014 (DOI: 10.1017/S002185961400094X). Not open access; view abstract. (G7010.02.01)
Wang S, Liang Z, Sun D, Dong F, Chen W, Wang H and Jing R (2015). Quantitative trait loci mapping for traits related to the progression of wheat flag leaf senescence. Journal of Agricultural Science Published online as FirstView Article: 24 September 2014 (DOI: 10.1017/S002185961400094X). Not open access; view abstract. (G7010.02.01)
Phosphorous efficiency and tolerance traits for selection of sorghum for performance in phosphorous-limited environments
Leiser WL, Rattunde HFW, Piepho H-P, Weltzien E, Diallo A, Toure A and Hausmann BIG (2015). Phosphorous efficiency and tolerance traits for selection of sorghum for performance in phosphorous-limited environments. Crop Science 55 Published online: 27 March 2015 (DOI: 10.2135/cropsci2014.05.0392). (G7010.03.03)
Abstract: Sorghum (Sorghum bicolor (L.) Moench) is widely cultivated in West Africa (WA) on soils with low phosphorus (P) availability. Large genetic variation for grain yield (GY) under low-P conditions was observed among WA sorghum genotypes, but information is lacking on the usefulness of P-tolerance ratios (relative performance in –P [no P fertilizer] vs. +P [with P fertilizer] conditions) and measures of P-acquisition and internal P-use efficiency as selection criteria for enhancing GY under low-P conditions. We evaluated 70 WA sorghum genotypes for GY performance under −P and +P conditions for 5 yr in two locations in Mali and assessed P acquisition (e.g., P content in biomass) and P-use efficiency (e.g., grain produced per unit P uptake) traits under −P and +P conditions in one site in 2010. Significant genetic variation existed for all P-tolerance ratios across multiple sites. Photoperiod-sensitive landrace genotypes showed significantly better P tolerance and less delay of heading under P-limited conditions compared with photoperiod-insensitive varieties. Genotypic correlations of P-tolerance ratios to GY under −P were moderate. Phosphorous acquisition and P-use efficiency traits independent of harvest index were of similar importance for GY under −P conditions in statistically independent trials. However grain-P and stover-P concentrations from one −P trial showed only weak correlations with GYs in statistically independent trials. Highest predicted gains for −P GY were obtained by theoretical index selection based on −P GY combined with P-use efficiency traits (e.g., low-grain P concentration). Such index selection is expected to achieve both increased sorghum productivity and P sustainability in the P-limited WA production systems.
Leiser WL, Rattunde HFW, Piepho H-P, Weltzien E, Diallo A, Toure A and Hausmann BIG (2015). Phosphorous efficiency and tolerance traits for selection of sorghum for performance in phosphorous-limited environments. Crop Science 55 Published online: 27 March 2015 (DOI: 10.2135/cropsci2014.05.0392). (G7010.03.03)
Abstract: Sorghum (Sorghum bicolor (L.) Moench) is widely cultivated in West Africa (WA) on soils with low phosphorus (P) availability. Large genetic variation for grain yield (GY) under low-P conditions was observed among WA sorghum genotypes, but information is lacking on the usefulness of P-tolerance ratios (relative performance in –P [no P fertilizer] vs. +P [with P fertilizer] conditions) and measures of P-acquisition and internal P-use efficiency as selection criteria for enhancing GY under low-P conditions. We evaluated 70 WA sorghum genotypes for GY performance under −P and +P conditions for 5 yr in two locations in Mali and assessed P acquisition (e.g., P content in biomass) and P-use efficiency (e.g., grain produced per unit P uptake) traits under −P and +P conditions in one site in 2010. Significant genetic variation existed for all P-tolerance ratios across multiple sites. Photoperiod-sensitive landrace genotypes showed significantly better P tolerance and less delay of heading under P-limited conditions compared with photoperiod-insensitive varieties. Genotypic correlations of P-tolerance ratios to GY under −P were moderate. Phosphorous acquisition and P-use efficiency traits independent of harvest index were of similar importance for GY under −P conditions in statistically independent trials. However grain-P and stover-P concentrations from one −P trial showed only weak correlations with GYs in statistically independent trials. Highest predicted gains for −P GY were obtained by theoretical index selection based on −P GY combined with P-use efficiency traits (e.g., low-grain P concentration). Such index selection is expected to achieve both increased sorghum productivity and P sustainability in the P-limited WA production systems.
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.
Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis
Leal-Bertioli S, Shirasawa K, Abernathy B, Moretzsohn M, Chavarro C, Clevenger J, Ozias-Akins P, Jackson S and Bertioli D (2015). Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 199(4):1093–1105 (DOI: 10.1534/genetics.115.174607). (G6010.01)
Abstract: Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes. Using this assumption, numerous linkage map and quantitative trait loci studies have been carried out. Here, with a systematic analysis of genotyping and gene expression data, we show that this assumption is not entirely valid. In fact, autotetraploid-like tetrasomic recombination is surprisingly frequent in recombinant inbred lines generated from a cross of cultivated peanut and an induced allotetraploid derived from peanut's most probable ancestral species. We suggest that a better, more predictive genetic model for peanut is that of a "segmental allotetraploid" with partly disomic, partly tetrasomic genetic behavior. This intermediate genetic behavior has probably had a previously overseen, but significant, impact on the genome and genetics of cultivated peanut.
Leal-Bertioli S, Shirasawa K, Abernathy B, Moretzsohn M, Chavarro C, Clevenger J, Ozias-Akins P, Jackson S and Bertioli D (2015). Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 199(4):1093–1105 (DOI: 10.1534/genetics.115.174607). (G6010.01)
Abstract: Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes. Using this assumption, numerous linkage map and quantitative trait loci studies have been carried out. Here, with a systematic analysis of genotyping and gene expression data, we show that this assumption is not entirely valid. In fact, autotetraploid-like tetrasomic recombination is surprisingly frequent in recombinant inbred lines generated from a cross of cultivated peanut and an induced allotetraploid derived from peanut's most probable ancestral species. We suggest that a better, more predictive genetic model for peanut is that of a "segmental allotetraploid" with partly disomic, partly tetrasomic genetic behavior. This intermediate genetic behavior has probably had a previously overseen, but significant, impact on the genome and genetics of cultivated peanut.
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.
