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.

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 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 Drought Tolerant near Isogenic Lines (NILs) of Pusa 44 Developed through Marker Assisted Introgression of qDTY2.1 and qDTY3.1 Enhances Yield under Reproductive Stage Drought Stress

Agriculture ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 64
Author(s):  
Priyanka Dwivedi ◽  
Naleeni Ramawat ◽  
Gaurav Dhawan ◽  
Subbaiyan Gopala Krishnan ◽  
Kunnummal Kurungara Vinod ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Grain Quality ◽  
Reproductive Stage ◽  
Recurrent Parent ◽  
Near Isogenic Lines ◽  
Improvement Project ◽  
Isogenic Lines ◽  
Drought Tolerant ◽  
Rice Improvement

Reproductive stage drought stress (RSDS) is detrimental for rice, which affects its productivity as well as grain quality. In the present study, we introgressed two major quantitative trait loci (QTLs), namely, qDTY2.1 and qDTY3.1, governing RSDS tolerance in a popular high yielding non-aromatic rice cultivar, Pusa 44, through marker-assisted backcross breeding (MABB). Pusa 44 is highly sensitive to RSDS, which restricts its cultivation across drought-prone environments. Foreground selection was carried out using markers, RM520 for qDTY3.1 and RM 521 for qDTY2.1. Background selection was achieved with 97 polymorphic SSR markers in tandem with phenotypic selection to achieve faster recurrent parent genome (RPG) recovery. Three successive backcrosses followed by three selfings aided RPG recoveries of 98.6% to 99.4% among 31 near isogenic lines (NILs). Fourteen NILs were found to be significantly superior in yield and grain quality under RSDS with higher drought tolerance efficiency (DTE) than Pusa 44. Among these, the evaluation of two promising NILs in the multilocational trial during Kharif 2019 showed that they were significantly superior to Pusa 44 under reproductive stage drought stress, while performing on par with Pusa 44 under normal irrigated conditions. These di-QTL pyramided drought-tolerant NILs are in the final stages of testing the All India Coordinated Rice Improvement Project varietal trials for cultivar release. Alternately, the elite drought-tolerant Pusa 44 NILs will serve as an invaluable source of drought tolerance in rice improvement.

A set of near-isogenic lines for blast resistance genes with an Indica-type rainfed lowland elite rice (Oryza sativa L.) genetic background

2011 ◽  
Vol 123 (1) ◽  
pp. 19-27 ◽  
Author(s):  
Yohei Koide ◽  
Leodegario A. Ebron ◽  
Hiroshi Kato ◽  
Hiroshi Tsunematsu ◽  
Mary Jeanie Telebanco-Yanoria ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Resistance Genes ◽  
Genetic Background ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Rainfed Lowland ◽  
Blast Resistance Genes

scholarly journals Maize nested introgression library provides evidence for the involvement of liguleless1 in resistance to northern leaf blight

2019 ◽  
Author(s):  
Judith M. Kolkman ◽  
Josh Strable ◽  
Kate Harline ◽  
Dallas E. Kroon ◽  
Tyr Wiesner-Hanks ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Analysis ◽  
Crop Improvement ◽  
Leaf Blight ◽  
Leaf Angle ◽  
Recurrent Parent ◽  
Near Isogenic Lines ◽  
Northern Leaf Blight ◽  
Leaf Architecture ◽  
Isogenic Lines

AbstractPlant disease resistance is largely governed by complex genetic architecture. In maize, few disease resistance loci have been characterized. Near-isogenic lines (NILs) are a powerful genetic tool to dissect quantitative trait loci (QTL). We analyzed an introgression library of maize near-isogenic lines (NILs), termed a nested NIL (nNIL) library for resistance to northern leaf blight (NLB) caused by the fungal pathogen Setosphaeria turcica. The nNIL library was comprised of 412 BC5F4 NILs that originated from 18 diverse donor parents and a common recurrent parent, B73. Single nucleotide polymorphisms identified through genotyping by sequencing (GBS) were used to define introgressions and for association analysis. NILs that conferred resistance and susceptibility to NLB were comprised of introgressions that overlapped known NLB QTL. Genome-wide association analysis and stepwise regression further resolved five QTL regions, and implicated several candidate genes, including Liguleless1 (Lg1), a key determinant of leaf architecture in cereals. Two independently-derived mutant alleles of lg1 inoculated with S. turcica showed enhanced susceptibility to NLB. In the maize nested association mapping population, leaf angle was positively correlated with NLB in five recombinant inbred line (RIL) populations, and negatively correlated with NLB in four RIL populations. This study demonstrates the power of a nNIL library combined with high density SNP coverage to resolve QTLs. Furthermore, the role of lg1 in leaf architecture and in resistance to NLB has important applications in crop improvement.Significance Statement (120 words)Understanding the genetic basis of disease resistance is important for crop improvement. We analyzed response to northern leaf blight (NLB) in a maize population consisting of 412 near-isogenic lines (NILs) derived from 18 diverse donor parents backcrossed to a recurrent parent, B73. NILs were genotyped by sequencing to detect introgressed segments. We identified NILs with greater resistance or susceptibility to NLB than B73. Genome-wide association analysis, coupled with stepwise regression, identified 5 candidate loci for NLB resistance, including the liguleless1 gene. The LIGULELESS1 transcription factor is critical in development of the leaf ligular region and influences leaf angle. We found that liguleless1 mutants are significantly more susceptible to NLB, uncovering a pleiotropic role for liguleless1 in development and disease resistance.

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.

scholarly journals Characterisation of a 4A QTL for Metribuzin Resistance in Wheat by Developing Near-Isogenic Lines

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1856
Author(s):  
Rudra Bhattarai ◽  
Hui Liu ◽  
Kadambot H. M. Siddique ◽  
Guijun Yan
Keyword(s):  
Weed Management ◽  
Quantitative Trait ◽  
Wheat Chromosome ◽  
Farming System ◽  
Triticum Aestivum L ◽  
Effective Control ◽  
Phenotypic Variance ◽  
Near Isogenic Lines ◽  
Resistant Parent ◽  
Isogenic Lines

Wheat (Triticum aestivum L.) production is constantly affected by weeds in the farming system. Chemical-based weed management is widely practiced; broad-spectrum herbicides such as metribuzin have been successfully used to control weeds in Australia and elsewhere of the world. Breeding metribuzin-resistant wheat through genetic improvement is needed for effective control of weeds. Quantitative trait loci (QTLs) mapping efforts identified a major QTL on wheat chromosome 4A, explaining up to 20% of the phenotypic variance for metribuzin resistance. The quantitative nature of inheritance of this QTL signifies the importance of near-isogenic lines (NILs), which can convert a quantitative trait into a Mendelian factor for better resolution of the QTL. In the current study, NILs were developed using a heterogeneous inbred family method combined with a fast generation-cycling system in a population of Chuan Mai 25 (resistant) and Ritchie (susceptible). Seven pairs of NILs targeting the 4A QTL for metribuzin resistance were confirmed with a molecular marker and phenotyping. The resistant allele from the resistant parent increased metribuzin resistance by 63–85% (average 69%) compared with the susceptible allele from the susceptible parent. Segregation analysis in the NIL pairs for thousand grain weight (TGW) (g), biomass per plant (kg), tillers per plant, plant height (cm), yield per plant, and powdery mildew visual score (0–9) indicated that these traits were linked with metribuzin resistance. Similarly, TGW was observed to co-segregate with metribuzin resistance in most confirmed NILs, signifying that the two traits are controlled by closely linked genes. The most contrasting NILs can be further characterised by transcriptomic and proteomic analyses to identify the candidate genes responsible for metribuzin resistance.

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