scholarly journals Validating a segment on chromosome 7 of japonica for establishing low-cadmium accumulating indica rice variety

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kai Wang ◽  
Tian-ze Yan ◽  
Shi-long Xu ◽  
Xu Yan ◽  
Qun-feng Zhou ◽  
...  
Keyword(s):  
Genetic Background ◽  
Safety Issue ◽  
Indica Rice ◽  
Rice Variety ◽  
Chromosome 7 ◽  
Recurrent Parent ◽  
Linkage Drag ◽  
Public Attention ◽  
Growth Duration ◽  
Cd Accumulation

AbstractCadmium (Cd) contamination of rice is a serious food safety issue that has recently been gaining significant public attention. Therefore, reduction of Cd accumulation in rice grains is an important objective of rice breeding. The use of favourable alleles of Cd accumulating genes using marker-assisted selection (MAS) is theoretically feasible. In this study, we validated a segment covering OsHMA3-OsNramp5-OsNramp1 on chromosome 7 of japonica for establishing low-cadmium accumulating indica rice variety. The OsHMA3-OsNramp5-OsNramp1jap haplotype significantly decreased grain Cd concentration in middle-season indica genetic background. The improved 9311 carrying the OsHMA3-OsNramp5-OsNramp1jap haplotype with recurrent parent genome recovery of up to 91.6% resulted in approximately 31.8% decrease in Cd accumulation in the grain and with no penalty on yield. There is a genetic linkage-drag between OsHMA3-OsNramp5-OsNramp1 jap and the gene conditioning heading to days (HTD) in the early-season indica genetic background. Because the OsHMA3-OsNramp5-OsNramp1-Ghd7jap haplotype significantly increases grain Cd concentration and prolongs growth duration, the linkage-drag between OsHMA3-OsNramp5-OsNramp1 and Ghd7 should be broken down by large segregating populations or gene editing. A novel allele of OsHMA3 was identified from a wide-compatibility japonica cultivar, the expression differences of OsNramp1 and OsNramp5 in roots might contribute the Cd accumulating variation between japonica and indica variety.

Comparative analysis of genetic background in eight near-isogenic wheat lines with different H genes conferring resistance to Hessian fly

Genome ◽  
2011 ◽  
Vol 54 (1) ◽  
pp. 81-89 ◽  
Author(s):  
S. S. Xu ◽  
C. G. Chu ◽  
M. O. Harris ◽  
C. E. Williams
Keyword(s):  
Genetic Background ◽  
Genetic Similarity ◽  
Triticum Aestivum L ◽  
Hessian Fly ◽  
Pedigree Analysis ◽  
Recurrent Parent ◽  
Linkage Drag ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
H Gene

Near-isogenic lines (NILs) are useful for plant genetic and genomic studies. However, the strength of conclusions from such studies depends on the similarity of the NILs’ genetic backgrounds. In this study, we investigated the genetic similarity for a set of NILs developed in the 1990s to study gene-for-gene interactions between wheat ( Triticum aestivum L.) and the Hessian fly ( Mayetiola destructor (Say)), an important pest of wheat. Each of the eight NILs carries a single H resistance gene and was created by successive backcrossing for two to six generations to susceptible T. aestivum ‘Newton’. We generated 256 target region amplification polymorphism (TRAP) markers and used them to calculate genetic similarity, expressed by the Nei and Li (NL) coefficient. Six of the NILs (H3, H5, H6, H9, H11, and H13) had the highly uniform genetic background of Newton, with NL coefficients from 0.97 to 0.99. However, genotypes with H10 or H12 were less similar to Newton, with NL coefficients of 0.86 and 0.93, respectively. Cluster analysis based on NL coefficients and pedigree analysis showed that the genetic similarity between each of the NILs and Newton was affected by both the number of backcrosses and the genetic similarity between Newton and the H gene donors. We thus generated an equation to predict the number of required backcrosses, given varying similarity of donor and recurrent parent. We also investigated whether the genetic residues of the donor parents that remained in the NILs were related to linkage drag. By using a complete set of ‘Chinese Spring’ nullisomic-tetrasomic lines, one third of the TRAP markers that showed polymorphism between the NILs and Newton were assigned to a specific chromosome. All of the assigned markers were located on chromosomes other than the chromosome carrying the H gene, suggesting that the genetic residues detected in this study were not due to linkage drag. Results will aid in the development and use of near-isogenic lines for studies of the functional genomics of wheat.

Marker assisted introgression of blast (Pi-2 and Pi-54) genes in to the genetic background of elite, bacterial blight resistant indica rice variety, Improved Samba Mahsuri

Euphytica ◽  
2016 ◽  
Vol 212 (2) ◽  
pp. 331-342 ◽  
Author(s):  
K. Ratna Madhavi ◽  
R. Rambabu ◽  
V. Abhilash Kumar ◽  
S. Vijay Kumar ◽  
J. Aruna ◽  
...  
Keyword(s):  
Genetic Background ◽  
Bacterial Blight ◽  
Indica Rice ◽  
Rice Variety

QTL for spikelet number from a high-yielding rice variety, Hoshiaoba, detected in an introgression line with the genetic background of an indica rice variety, IR64

Euphytica ◽  
2013 ◽  
Vol 192 (1) ◽  
pp. 97-106 ◽  
Author(s):  
Yohei Koide ◽  
Daisuke Fujita ◽  
Analiza G. Tagle ◽  
Kazuhiro Sasaki ◽  
Tsutomu Ishimaru ◽  
...  
Keyword(s):  
Genetic Background ◽  
Indica Rice ◽  
Rice Variety ◽  
Introgression Line ◽  
Spikelet Number

scholarly journals Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, “Pusa Basmati 1121”

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Nitasha Grover ◽  
Aruna Kumar ◽  
Ashutosh Kumar Yadav ◽  
S. Gopala Krishnan ◽  
Ranjith Kumar Ellur ◽  
...  
Keyword(s):  
Genetic Background ◽  
Cooking Quality ◽  
Rice Variety ◽  
Basmati Rice ◽  
Recurrent Parent ◽  
Quality Traits ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Herbicide Tolerant ◽  
Grain And Cooking Quality

Abstract Background Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. Results We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) “Robin” into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC4F4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. Conclusion Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.

scholarly journals Marker assisted development and characterization of herbicide tolerant Near Isogenic Lines of a mega Basmati rice variety, “Pusa Basmati 1121”

2020 ◽  
Author(s):  
Nitasha Grover ◽  
Aruna Kumar ◽  
Ashutosh Kumar Yadav ◽  
Gopala Krishnan S. ◽  
Ranjith Kumar Ellur ◽  
...  
Keyword(s):  
Genetic Background ◽  
Cooking Quality ◽  
Rice Variety ◽  
Basmati Rice ◽  
Recurrent Parent ◽  
Quality Traits ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Herbicide Tolerant ◽  
Grain And Cooking Quality

Abstract Background Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. Results We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase ( AHAS ) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) “Robin” into the genetic background of an elite popular Basmati rice variety Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC 4 F 4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. Conclusion Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.

scholarly journals Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.)

2012 ◽  
Vol 62 (1) ◽  
pp. 18-26 ◽  
Author(s):  
Daisuke Fujita ◽  
Analiza G. Tagle ◽  
Leodegario A. Ebron ◽  
Yoshimichi Fukuta ◽  
Nobuya Kobayashi
Keyword(s):  
Oryza Sativa ◽  
Genetic Background ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Rice Variety ◽  
Near Isogenic Lines ◽  
Spikelet Number ◽  
Isogenic Lines

scholarly journals Enhancing backcross programs through increased recombination

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Elise Tourrette ◽  
Matthieu Falque ◽  
Olivier C. Martin
Keyword(s):  
Recombination Rate ◽  
Genetic Background ◽  
Recurrent Parent ◽  
Linkage Drag ◽  
Donor Genome ◽  
Recurrent Parent Genome ◽  
Foreground Selection ◽  
Two Generations ◽  
Donor Parent ◽  
Trait Locus

Abstract Background Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters. Results In this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental. Conclusions Depending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation.

scholarly journals Marker assisted development and characterization of non-GM herbicide tolerant Near Isogenic Lines of a mega Basmati rice variety, “Pusa Basmati 1121”

2020 ◽  
Author(s):  
Nitasha Grover ◽  
Aruna Kumar ◽  
Ashutosh Kumar Yadav ◽  
Gopala Krishnan S. ◽  
Ranjith Kumar Ellur ◽  
...  
Keyword(s):  
Genetic Background ◽  
Cooking Quality ◽  
Rice Variety ◽  
Basmati Rice ◽  
Recurrent Parent ◽  
Quality Traits ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Herbicide Tolerant ◽  
Grain And Cooking Quality

Abstract Background Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. Results We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) “Robin” into the genetic background of an elite popular Basmati rice variety Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC4F4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. Conclusion Overall, the present study reports successful development of non-GM HT NILs in the genetic background of popular Basmati rice variety PB 1121 by introgression of mutated AHAS allele. This is the first report of the development of HT rice in India. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.

scholarly journals Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 804
Author(s):  
Me-Sun Kim ◽  
Ju-Young Yang ◽  
Ju-Kyung Yu ◽  
Yi Lee ◽  
Yong-Jin Park ◽  
...  
Keyword(s):  
Genetic Background ◽  
Amylose Content ◽  
Yield Potential ◽  
Eating Quality ◽  
Breeding Cycle ◽  
Recurrent Parent ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Genome Wide ◽  
Cooking And Eating Quality

The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.

Sign in / Sign up

Export Citation Format

Share Document