Journal articles 2014
Documents
Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects
Bohra A, Pandey MK, Jha UC, Singh B, Singh IP, Datta D, Chaturvedi SK, Nadarajan N and Varshney RK (2014). Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects. Theoretical and Applied Genetics 127(6):1263–1291 (DOI: 10.1007/s00122-014-2301-3).
Key message: Given recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops.
Abstract: The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.
Bohra A, Pandey MK, Jha UC, Singh B, Singh IP, Datta D, Chaturvedi SK, Nadarajan N and Varshney RK (2014). Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects. Theoretical and Applied Genetics 127(6):1263–1291 (DOI: 10.1007/s00122-014-2301-3).
Key message: Given recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops.
Abstract: The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.
Full article
Genotypic performance in multi-location on-farm trials for evaluation of different on-station screening methods for drought-prone rainfed lowland rice in Lao PDR
Xangsayasane P, Fukai S, Mitchell JH, Jongdee B, Jothityangkoon D, Pantuwan G and Inthapanya P (2014). Genotypic performance in multi-location on-farm trials for evaluation of different on-station screening methods for drought-prone rainfed lowland rice in Lao PDR. Field Crops Research 160:1–11 (DOI: 10.1016/j.fcr.2014.02.009). Not open access; view abstract. (G3008.06)
Xangsayasane P, Fukai S, Mitchell JH, Jongdee B, Jothityangkoon D, Pantuwan G and Inthapanya P (2014). Genotypic performance in multi-location on-farm trials for evaluation of different on-station screening methods for drought-prone rainfed lowland rice in Lao PDR. Field Crops Research 160:1–11 (DOI: 10.1016/j.fcr.2014.02.009). Not open access; view abstract. (G3008.06)
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)
Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding
Varshney RK, Terauchi R, McCouch SR (2014). Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding PLoS Biology 12(6):e1001883 (DOI: 10.1371/journal.pbio.1001883).
Abstract: Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.
Varshney RK, Terauchi R, McCouch SR (2014). Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding PLoS Biology 12(6):e1001883 (DOI: 10.1371/journal.pbio.1001883).
Abstract: Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.
High throughput screening of rooting depth in rice using buried herbicide
Al-Shugeairy Z, Islam MS, Shrestha R, Al-Ogaidi F, Norton GJ and Price AH (2014). High throughput screening of rooting depth in rice using buried herbicide. Annals of Applied Biology 165(1):96–107 (DOI: 10.1111/aab.12118). Not open access; view abstract. (G3008.06)
Al-Shugeairy Z, Islam MS, Shrestha R, Al-Ogaidi F, Norton GJ and Price AH (2014). High throughput screening of rooting depth in rice using buried herbicide. Annals of Applied Biology 165(1):96–107 (DOI: 10.1111/aab.12118). Not open access; view abstract. (G3008.06)
Identification of QTLs for seedling vigor in winter wheat
Li X-M, Chen X-M, Xiao Y-G, Xia X-C, Wang D-S, He Z-H and Wang H-J (2014). Identification of QTLs for seedling vigor in winter wheat. Euphytica 198(2):199–209 (DOI: 10.1007/s10681-014-1092-6). Not open access; view abstract. (G7010.02.01)
Li X-M, Chen X-M, Xiao Y-G, Xia X-C, Wang D-S, He Z-H and Wang H-J (2014). Identification of QTLs for seedling vigor in winter wheat. Euphytica 198(2):199–209 (DOI: 10.1007/s10681-014-1092-6). Not open access; view abstract. (G7010.02.01)
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.
Linking root traits and grain yield for rainfed rice in sub-Saharan Africa: response of Oryza sativa x Oryza glaberrima introgression lines under drought
Kijoji AA, Nchimbi-Msolla S, Kanyeka ZL, Serraj R and Henry A (2014). Linking root traits and grain yield for rainfed rice in sub-Saharan Africa: response of Oryza sativa x Oryza glaberrima introgression lines under drought. Field Crops Research 165:25–35 (DOI: 10.1016/j.fcr.2014.03.019). Not open access; view abstract. (G3008.06)
Kijoji AA, Nchimbi-Msolla S, Kanyeka ZL, Serraj R and Henry A (2014). Linking root traits and grain yield for rainfed rice in sub-Saharan Africa: response of Oryza sativa x Oryza glaberrima introgression lines under drought. Field Crops Research 165:25–35 (DOI: 10.1016/j.fcr.2014.03.019). Not open access; view abstract. (G3008.06)
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.
Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)
Varshney RK, Pandey MK, Pasupuleti J, Nigam SN, Sudini H, Gowda MVC, Sriswathi M, Radhakrishnan T, Manohar SS and Nagesh P (2014). Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theoretical and Applied Genetics. Published online: 14 June 2014 (DOI: 10.1007/s00122-014-2338-3).
Key message: Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield.
Abstract: Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.
Varshney RK, Pandey MK, Pasupuleti J, Nigam SN, Sudini H, Gowda MVC, Sriswathi M, Radhakrishnan T, Manohar SS and Nagesh P (2014). Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theoretical and Applied Genetics. Published online: 14 June 2014 (DOI: 10.1007/s00122-014-2338-3).
Key message: Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield.
Abstract: Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.
