Stacking of Pup1 QTL for Low Soil Phosphorus Tolerance and Bacterial Blight Resistance Genes in the Background of APMS6B, the Maintainer Line of Rice Hybrid DRRH-3

Phosphorus (P) is one of the macro nutrients essential for plant growth and development. Rice (Oryza sativa L.) is sensitive to P starvation and its deficiency influences many key plant functions which results in crop yield penalty. Although the hybrid rice segment is well-known for its yield heterosis, P deficiency and bacterial leaf blight (BLB) diseases are the evident limitations. APMS6B, the female parent of DRRH-3 is susceptible to low P and bacterial blight disease. In the present study, the improvement of APMS6B to P starvation and resistance to bacterial leaf blight (BB) was carried out using marker-assisted backcross breeding (MABB) approach. Kasalath (+ Pup1 QTL) was used as donor and a promising IL (ATR 594-1) at BC1 F4 generation was identified with 81.15% RPGR. Concurrently, this IL was intercrossed with GU-2 (+ Xa21 and Xa38 ). Hybridity of Intercross F1s (ICF1) was confirmed through foreground selection having maximum RPGR (88.29%) and were selfed to produce ICF2. The resultant progenies were phenotyped for BB using Xoo inoculum (IX-020), simultaneously genotyped with gene specific functional SSR markers for Xa21 and Xa38. The identified BB resistant plants were subjected to foreground selection for Pup1. Four promising ICF3 plants (BP-10-1, BP-10-3, BP-10-5 and BP-10-15 with Xa21, Xa38 and Pup1) along with parents and checks were screened both in low P plot (<2 kg P2O5 ha-1 ) as well as in normal plot (>25 kg P2O5 ha-1) during dry and wet seasons 2018. Based on the field evaluation, four promising intercrossed lines were identified with better root architecture in terms of root length and root volume. In addition, less % reduction in grain yield (39.10%) under P starvation and less susceptibility indices values (<1) for BB were observed. These lines may be utilized in the CMS conversion programme and development of climate resilient, biotic and abiotic tolerant rice hybrids.

Enhancing backcross programs through increased recombination

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.

Marker Assisted Gene Pyramiding for Bacterial Blight Resistance in Some Improved Rice Genotypes

Bacterial blight is one of the major diseases of rice, causing huge economic loss to the rice farmers around the world. In the present study, marker assisted selection (MAS) was used to pyramid broad spectrum resistance genes (Xa33 and Xa38) into two improved rice genotypes (ADT 47 and ASD 16) which already have some bacterial blight resistance genes (xa5, xa13 and Xa21). The rice genotypes FBRI-15 and PR114 were used as donors of Xa33 and Xa38 genes respectively. The marker RMWR7.1 linked to Xa33 and the sequenced-tagged site marker Os04g53050-1 specific to Xa38 were used for foreground selection. True F1 hybrids were selected using the polymorphic markers. Out of one hundred and thirty-seven SSR markers, forty-two were polymorphic for improved ADT 47 x FBRI-16 and forty-six were polymorphic for Improved ASD 16 x PR114. The polymorphic markers were used for background selection. Foreground selection revealed that a single F1 plant was heterozygote in Improved ADT 47 X FBRI-15 whereas two plants were heterozygotes in Improved ASD 16 x PR114. At BC1F1, one and three plants were found to be heterozygous respectively for Improved ADT 47 x FBRI-15 and Improved ASD 16 x PR114. At BC2F1, single plant each was found heterozygous from the two crosses. In the final BC3F1 population, one heterozygote each was obtained from the two crosses. In BC3F1, plant number 11 had 92.80% parental genome recovery in the Improved ADT 47 x FBRI-15, whereas plant no 16 had 91.33% parental genome recovery in the Improved ASD 16 x PR114

Enhancing backcross programs through increased recombination

ABSTRACTIntrogression of a QTL by successive backcrosses is a strategy that can be used to improve elite lines (recurrent parent) by bringing in 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 one selects for the donor allele at the QTL, the elimination of the donor genome in the neighborhood of that QTL will be much slower (linkage drag). Using markers to monitor the genome around the QTL and in the background can accelerate the return to the recurrent parent genome. The success of an introgression will partly depend 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 aspects of recombination. Here, we assess, by simulation, their effect on the efficiency of introgression programs by studying the reduction of the linkage drag and the recovery of the recurrent genome. The selection schemes we simulate 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 was initially lacking crossovers, increasing the recombination rate can decrease the linkage drag nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region already rich in crossovers then increasing recombination proves to be detrimental.Key messageIn breeding programs, recombination is essential for introgression, but introducing more crossovers is beneficial only when the target is in a cold region, otherwise it is detrimental.

Molecular Evaluation for Drought Tolerant Using Marker Assisted Breeding Method

The sustainability and increasing the national rice production require the readiness of food and agriculture sector cope with the impacts of climate change, land degradation, drought area, sloping production and the raising of population growth. Adaptation plays an important role in ensuring the sustainability of food security. This research aimed to develop drought-tolerant variety of Inpari 30 (submergence tolerance variety) and Situ Bagendit through marker-assisted backcrossing-through pyramiding gene of identified QTLs for foreground selection and to explore SSRs and 6K SNPs for background selection distributed in 12 rice chromosome of drought tolerant donor (Cabacu) and recipient rice (Inpari 30 and Situ Bagendit). The foreground selection revealed that flanking SSRs of each QTLs (qRPF2.1, qGPP2.1, qSPP4.1 and Sub1) was less than 2 cM. The background selection through polymorphic survey of Rice 6K SNP primers revealed 2457 (53,3%) polymorphic SNPs on Inpari 30 vs Cabacu and 2563 (55,6%) polymorphic SNPs on Situ Bagendit vs Cabacu with the average distance about 0.74 cM/chromosome. The genotypic selection of F1 Inpari 30/Cabacu and F1 Situ Bagendit/Cabacu have already in heterozygote condition for these 4 QTLs target. These lines was continued for backcross breeding to develop BC1F1 Inpari 30/Cabacu and BC1F1 Situ Bagendit/Cabacu generation.

Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1”

Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.