Genetic Enhancement for Biotic Stress Resistance in Basmati Rice through Marker-Assisted Backcross Breeding
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ABSTRACT:
SUBMITTER: Singh G
PROVIDER: S-EPMC10671030 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Breeding low phytate crops is the most viable solution to tackle mineral deficiencies. The objective of the present study was to develop high yielding, low phytate (lpa) basmati rice cultivars. Three homozygous lpa mutants, Lpa5, Lpa9, and Lpa59, were developed through induced mutations (gamma rays 60Co) and identified by colorimetric and High Performance Liquid Chromatography (HPLC) analysis. These mutants showed 54%-63% reduction in phytic acid but had poor germination and yield. To improve these traits, hybridization and back cross breeding involving Lpa5, Lpa59, and parent cultivar Super Basmati were performed and F2:3, F3:4, BC1F2:3, and BC1F3:4 generations were developed and screened to target the objective. Within the F2:3, homozygous (226), heterozygous (65), and wild type (46) lpa recombinants were identified. Within the homozygous lpa category, four recombinants (Lpa5, Lpa6, Lpa7, and Lpa30) showed improved germination. Within the F3:4 generation, 86 homozygous lpa recombinants were identified. Further selection, on the basis of better plant type and the low phytate trait resulted in the selection of 38 recombinants. Grain quality and cooking characteristics of these selected recombinants were comparable as compared to parent cultivar. Within the BC1F2:3 generations, two homozygous Lpa recombinant lines, Lpa141, and Lpa205, were selected out of 220. Screening of the BC1F3:4 generation for the desirable agronomic and low phytate trait also resulted in the selection of two homozygous lines. Finally, seven recombinants i.e. Lpa12-3, Lpa111-1, Lpa141, Lpa56-3, Lpa53-4, Lpa99-2, and Lpa205-4 out of 42 homozygous low phytate lines were selected on the basis of yield improvement (4%-18%) as compared to parent cultivar. Association analysis suggested that further selection based on primary branches per plant, panicle length and productive tillers per plant would further improve the paddy yield. For molecular characterization of the Lpa trait, previously reported Lpa1-CAPS and Lpa1-InDel and functional molecular markers were applied. Results indicated the absence of the Z9B-Lpa allele and XS-Lpa mutation in the OsMRP5 gene in tested mutants, possibly suggesting that there may be new mutations or novel alleles in tested mutants that need to be identified and then fine mapped for subsequent utilization. To our knowledge, this is the first report of low phytic acid rice mutant development and their improved germination and yield through backcross breeding in basmati rice.
| S-EPMC6901921 | biostudies-literature
Project description:BACKGROUND:Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (Pi9), bacterial leaf blight (BLB) (Xa4, xa5, xa13, Xa21), brown planthopper (BPH) (Bph3, Bph17), gall midge (GM) (Gm4, Gm8) and QTLs for drought tolerance (qDTY1.1 and qDTY3.1) through marker-assisted forward breeding (MAFB) approach. RESULT:Seven introgression lines (ILs) possessing a combination of seven to ten genes/QTLs for different biotic and abiotic stresses have been developed using marker-assisted selection (MAS) breeding method in the background of Swarna with drought QTLs. These ILs were superior to the respective recurrent parent in agronomic performance and also possess preferred grain quality with intermediate to high amylose content (AC) (23-26%). Out of these, three ILs viz., IL1 (Pi9+ Xa4+ xa5+ Xa21+ Bph17+ Gm8+ qDTY1.1+ qDTY3.1), IL6 (Pi9+ Xa4+ xa5+ Xa21+ Bph3+ Bph17+ Gm4+ Gm8+ qDTY1.1+ qDTY3.1) and IL7 (Pi9+ Xa4+ xa5+ Bph3+ Gm4+ qDTY1.1+ qDTY3.1) had shown resistance\tolerance for multiple biotic and abiotic stresses both in the field and glasshouse conditions. Overall, the ILs were high yielding under various stresses and importantly they also performed well in non-stress conditions without any yield penalty. CONCLUSION:The current study clearly illustrated the success of MAS in combining tolerance to multiple biotic and abiotic stresses while maintaining higher yield potential and preferred grain quality. Developed ILs with seven to ten genes in the current study showed superiority to recurrent parent Swarna+drought for multiple-biotic stresses (blast, BLB, BPH and GM) together with yield advantages of 1.0 t ha- 1 under drought condition, without adverse effect on grain quality traits under non-stress.
| S-EPMC7260318 | biostudies-literature
Project description:The elite Indian rice variety, Naveen is highly susceptible to major biotic and abiotic stresses such as blast, bacterial blight (BB), gall midge (GM) and drought which limit its productivity in rainfed areas. In the present study, a combined approach of marker-assisted forward (MAFB) and back cross (MABC) breeding was followed to introgress three major genes, viz., Pi9 for blast, Xa21 for bacterial blight (BB), and Gm8 for gall midge (GM) and three major QTLs, viz., qDTY1.1, qDTY2.2 and qDTY4.1 conferring increased yield under drought in the background of Naveen. At each stage of advancement, gene-based/linked markers were used for the foreground selection of biotic and abiotic stress tolerant genes/QTLs. Intensive phenotype-based selections were performed in the field for identification of lines with high level of resistance against blast, BB, GM and drought tolerance without yield penalty under non-stress situation. A set of 8 MAFB lines and 12 MABC lines with 3 to 6 genes/QTLs and possessing resistance/tolerance against biotic stresses and reproductive stage drought stress with better yield performance compared to Naveen were developed. Lines developed through combined MAFB and MABC performed better than lines developed only through MAFB. This study exemplifies the utility of the combined approach of marker-assisted forward and backcrosses breeding for targeted improvement of multiple biotic and abiotic stress resistance in the background of popular mega varieties.
| S-EPMC8412243 | biostudies-literature
Project description:The gram pod borer Helicoverpa armigera is a major constraint to chickpea (Cicer arietinum L.) production worldwide, reducing crop yield by up to 90%. The constraint is difficult to overcome as chickpea germplasm including wild species either lacks pod borer resistance or if possessing resistance is cross-incompatible. This study describes conversion of elite but pod borer-susceptible commercial chickpea cultivars into resistant cultivars through introgression of cry1Ac using marker-assisted backcross breeding. The chickpea cultivars (PBG7 and L552) were crossed with pod borer-resistant transgenic lines (BS 100B and BS 100E) carrying cry1Ac that led to the development of BC1F1, BC1F2, BC1F3, BC2F1, BC2F2, and BC2F3 populations from three cross combinations. The foreground selection revealed that 35.38% BC1F1 and 8.4% BC1F2 plants obtained from Cross A (PBG7 × BS 100B), 50% BC1F1 and 76.5% BC1F2 plants from Cross B (L552 × BS 100E), and 12.05% BC2F2 and 82.81% (average) BC2F3 plants derived from Cross C (PBG7 × BS 100E) carried the cry1Ac gene. The bioassay of backcross populations for toxicity to H. armigera displayed up to 100% larval mortality. BC1F1 and BC1F2 populations derived from Cross B and BC2F3 population from Cross C segregated in the Mendelian ratio for cry1Ac confirmed inheritance of a single copy of transgene, whereas BC1F1 and BC1F2 populations obtained from Cross A and BC2F2 population from Cross C exhibited distorted segregation ratios. BC1F1 plants of Cross A and Cross B accumulated Cry1Ac protein ranging from 11.03 to 11.71 µgg-1 in leaf tissue. Cry1Ac-positive BC2F2 plants from Cross C demonstrated high recurrent parent genome recovery (91.3%) through background selection using SSR markers and phenome recovery of 90.94%, amongst these 30% plants, were homozygous for transgene. The performance of BC2F3 progenies derived from homozygous plants was similar to that of the recurrent parent for main agronomic traits, such as number of pods and seed yield per plant. These progenies are a valuable source for H. armigera resistance in chickpea breeding programs.
| S-EPMC9039336 | biostudies-literature
Project description:Blast disease and cold stress are two major yield-limiting factors for rice under temperate climates. Marker-assisted backcross breeding approach (MABB) was employed for the improvement of blast resistance in a popular cold-tolerant variety 'Himalaya741' by introgressing a broad-spectrum resistance locus Pi9 from a Basmati donor PB1637. A combined use of phenotypic selection and marker-based genotypic selection ensured speedy reconstitution of the recurrent parent genome (RPG) in backcross progenies; RPG recovery in most of the progenies was > 96% with three progenies namely, HPU-1-33, -38 and -49 showing complete recovery of recurrent parent genome. Notwithstanding a very higher recovery rate of RPG in introgression lines, the lines still inherited a large linkage block > 13.3 Mb with Pi9 from the donor line PB1637. The donor chromosome segments co-inherited with Pi9 gene, however, did not have any adverse effect on the agronomic performance of the Pi9 introgression lines. Of the eight genetically superior Pi9 introgression lines identified, two exhibited resemblance to Himalaya 741 for most of the agronomic traits in addition to having superior grain length and tiller number. The introgression line HPU-1-81 displayed 44% yield superiority over recurrent parent, primarily due to improvement in yield-contributing traits, namely, tiller number, panicle length, thousand-seed-weight and grain length. All the Pi9 introgression lines displayed a high level of resistance comparable to PB1637 against two highly virulent blast races, which collectively displayed compatibility to 15 different major resistance genes. The introgression lines also possessed reproductive stage cold tolerance similar to recurrent parent under prevailing cold stress conditions. The agronomically superior Pi9 introgression lines developed herein are expected to provide a comparable or better substitute to blast susceptible variety Himalaya 741 for extenuating losses due to cold stress and blast disease.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-022-03244-w.
| S-EPMC9276897 | biostudies-literature
Project description:The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants produced by breeding through Marker Assisted Backcrossing (MAB).Focusing on transcriptome variation and perturbation to signaling pathways, we assessed the molecular and biological aspects of substantial equivalence, a general principle for food safety endorsed by the Food and Agricultural Organization and the World Health Organization, between a transgenic crop and a plant from MAB breeding. We compared a transgenic rice line (DXT) and a MAB rice line (DXB), both of which contain the gene Xa21 providing resistance to bacterial leaf blight. By using Next-Generation sequencing data of DXT, DXB and their parental line (D62B), we compared the transcriptome variation of DXT and DXB. Remarkably, DXT had 43% fewer differentially expressed genes (DEGs) than DXB. The genes exclusively expressed in DXT and in DXB have pathogen and stress defense functions. Functional categories of DEGs in DXT were comparable to that in DXB, and seven of the eleven pathways significantly affected by transgenesis were also perturbed by MAB breeding.These results indicated that the transgenic rice and rice from MAB breeding are substantial equivalent at the transcriptome level, and paved a way for further study of transgenic rice, e.g., understanding the chemical and nutritional properties of the DEGs identified in the current study.
| S-EPMC4007521 | biostudies-literature
Project description:Bacterial blight (BB) disease and submergence due to flash flood are the two major constraints for achieving higher yield from rainfed lowland rice. Marker-assisted backcross breeding was followed to develop submergence tolerant and durable BB resistant variety in the background of popular cultivar 'Swarna'. Four BB resistance genes viz., Xa4, xa5, xa13, Xa21 and Sub1 QTL for submergence tolerance were incorporated into the mega variety. Foreground selection for the five target genes was performed using closely linked markers and tracked in each backcross generations. Background selection in plants carrying the target genes was performed by using 100 simple sequence repeat markers. Amongst backcross derivatives, the plant carrying five target genes and maximum recurrent parent genome content was selected in each generation and hybridized with recipient parent. Eighteen BC3F2 plants were obtained by selfing the selected BC3F1 line. Amongst the pyramided lines, 3 lines were homozygous for all the target genes. Bioassay of the 18 pyramided lines containing BB resistance genes was conducted against different Xoo strains conferred very high levels of resistance to the predominant isolates. The pyramided lines also exhibited submergence tolerance for 14 days. The pyramided lines were similar to the recurrent parent in 14 morpho-quality traits.
| S-EPMC6728354 | biostudies-literature
Project description:BackgroundDirect-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.ResultsWe 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.ConclusionOverall, 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.
| S-EPMC7492307 | biostudies-literature
Project description:Manipulation of flowering time for adaptation through natural or genetic approaches may combat heat-stress damage that occurs at the reproductive stages in production conditions. HD2733, a popular wheat variety of the eastern plains of India, is largely sensitive to heat stress. Therefore, the current study aims to improve heat tolerance of HD2733 by introgression of QTLs associated with early anthesis and high kernel weight linked to markers Xbarc186 and Xgwm190, respectively, through marker-assisted backcross breeding (MABB) from a tolerant donor, WH730. A total of 124 simple sequence repeat (SSR) markers distributed evenly across the genome were used for the background selection. The alleles of Xbarc186 and Xgwm190 were fixed in BC2F1 and BC1F2 generations by selecting individual plants heterozygous for both marker loci and backcrossed with HD2733 and simultaneously selfed to generate BC2F1 and BC1F2 populations, respectively. Furthermore, the selected BC1F2 were selfed to generate the BC1F4 population. By background screening, a total of 39 BC2F3 and 21 BC1F4 families homozygous for the targeted QTLs with 90.9-97.9% and 86.8-88.3% RPG recoveries were selected. The best performing 17 BC2F3 and 10 BC1F4 lines were evaluated for various morpho-physiological traits. Phenotypic evaluation and multi-location trials of the introgressed lines under late sown conditions led to the selection of three promising lines with early anthesis and higher grain yield. The improved lines will serve as an excellent genetic material for functional genomics and expression studies to understand the molecular mechanisms and pathways underlying the stress tolerance.
| S-EPMC9785257 | biostudies-literature
Project description:Poplar is one of the most important forest trees because of its high economic value. Thanks to the fast-growing rate, easy vegetative propagation and transformation, and availability of genomic resources, poplar has been considered the model species for forest genetics, genomics, and breeding. Being a field-growing tree, poplar is exposed to environmental threats, including biotic stresses that are becoming more intense and diffused because of global warming. Current poplar farming is mainly based on monocultures of a few elite clones and the expensive and long-term conventional breeding programmes of perennial tree species cannot face current climate-change challenges. Consequently, new tools and methods are necessary to reduce the limits of traditional breeding related to the long generation time and to discover new sources of resistance. Recent advances in genomics, marker-assisted selection, genomic prediction, and genome editing offer powerful tools to efficiently exploit the Populus genetic diversity and allow enabling molecular breeding to support accurate early selection, increasing the efficiency, and reducing the time and costs of poplar breeding, that, in turn, will improve our capacity to face or prevent the emergence of new diseases or pests.
| S-EPMC9370193 | biostudies-literature