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 Enhancing backcross programs through increased recombination

2020 ◽  
Author(s):  
Elise Tourrette ◽  
Matthieu Falque ◽  
Olivier C. Martin
Keyword(s):  
Recurrent Parent ◽  
Linkage Drag ◽  
Background Selection ◽  
Cold Region ◽  
Donor Genome ◽  
Breeding Programs ◽  
Recurrent Parent Genome ◽  
Foreground Selection ◽  
Two Generations ◽  
Donor Parent

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.

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 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 Verification and dissection of one quantitative trait locus for grain size and weight on chromosome 1 in rice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi-chen Cheng ◽  
Guan Li ◽  
Man Yin ◽  
Tosin Victor Adegoke ◽  
Yi-feng Wang ◽  
...  
Keyword(s):  
Grain Size ◽  
Quantitative Trait ◽  
Genetic Background ◽  
Molecular Design ◽  
Chromosome 1 ◽  
Recurrent Parent ◽  
Isogenic Line ◽  
Growing Seasons ◽  
Ril Population ◽  
Trait Locus

AbstractGrain size and weight are the key traits determining rice quality and yield and are mainly controlled by quantitative trait loci (QTL). In this study, one minor QTL that was previously mapped in the marker interval of JD1009-JD1019 using the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population, qTGW1-2, was validated to regulate grain size and weight across four rice-growing seasons using twenty-one near isogenic line (NIL)-F2 populations. The twenty-one populations were in two types of genetic background that were derived from the same parents HHZ and JZ1560. Twelve F9, F10 or F11 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were developed from one residual heterozygote (RH) in the HHZ/JZ1560 RIL population, and the remaining nine BC3F3, BC3F4 or BC3F5 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were constructed through consecutive backcrosses to the recurrent parent HHZ followed with marker assistant selection in each generation. Based on the QTL analysis of these genetic populations, qTGW1-2 was successfully confirmed to control grain length, width and weight and further dissected into two QTLs, qTGW1-2a and qTGW1-2b, which were respectively narrowed down to the marker intervals of JD1139-JD1127 (~ 978.2-kb) and JD1121-JD1102 (~ 54.8-kb). Furthermore, the two types of NIL-F2 populations were proved to be able to decrease the genetic background noise and increase the detection power of minor QTL. These results provided an important basis for further map-based cloning and molecular design breeding with the two QTLs in rice.

scholarly journals Characterization of Donor Genome Segments of BC2 and BC4 Way Rarem x Oryzica Llanos-5 Progenies Detected by SNP Markers

2016 ◽  
Vol 8 (1) ◽  
pp. 1
Author(s):  
Wening Enggarini ◽  
Surjono H. Sudjahjo ◽  
Trikoesoemaningtyas Trikoesoemaningtyas ◽  
Sriani Sujiprihati ◽  
Utut Widyastuti ◽  
...  
Keyword(s):  
Rice Genome ◽  
Snp Markers ◽  
Genome Segment ◽  
Recurrent Parent ◽  
Donor Genome ◽  
Simple Method ◽  
Advanced Backcross ◽  
Donor Segment ◽  
A Genome ◽  
Donor Parent

<p>Plant breeders<br />make a succession of backcrosses to introgress a character<br />from a donor parent into genomic background of a recurrent<br />parent. In several backcrossing, the proportion of a genome<br />tends to return almost fully to recurrent parent, except the<br />small donor genome segment harboring the character of<br />interest. The estimation of the proportion donor segment<br />through backcross generations has been analyzed<br />theoretically using complex mathematical simulations. In<br />this study, the proportion of donor introgression segments<br />were directly analyzed in advanced backcross populations,<br />BC2F7 and BC4F2. The analysis was done by using a set of<br />single nucleotide polymorphism (SNP) markers covering the<br />entire rice genome. Of the 384 SNP markers we found 124<br />markers which provide polymorphism between recurrent<br />parent, Way Rarem and Oryzica Llanos-5 as donor parent.<br />But only 55 SNP markers could detect Oryzica Llanos-5<br />alleles in BC2F7 and BC4F2 progenies. The result of this<br />analysis demonstrated that the average of donor segment<br />number was 14.5 in BC2F7 and 12.3 in BC4F2. It was reduced<br />15% from BC2F7 to BC4F2. The average of donor segment<br />length was 31.2 cM (centiMorgan) in BC2F7 and 8.79 cM in<br />BC4F2. It was decreased 72% during twice backcrossing. The<br />average of donor genome size was 343.95 cM in BC2F7 and<br />71.35 cM in BC4F2, which means there was 79% decrease<br />from BC2F7 to BC4F2. These results offered a simple method<br />to describe the proportion of target genome segment from<br />donor parent. It was required as one of the main selection<br />criteria in backcross programs.</p>

scholarly journals Foreground selection through SSRs markers for the development of salt tolerant rice variety

2014 ◽  
Vol 11 (1) ◽  
pp. 67-72 ◽  
Author(s):  
U Mondal ◽  
MSR Khanom ◽  
L Hassan ◽  
SN Begum
Keyword(s):  
Rice Variety ◽  
Rice Cultivar ◽  
Susceptible Variety ◽  
Recurrent Parent ◽  
Salt Tolerant ◽  
Foreground Selection ◽  
Donor Parent ◽  
Ssrs Markers ◽  
Level Of Selection ◽  
Marker Assisted Backcrossing

Salinity is a great problem for rice production worldwide incurring substantial yield loss; a great threat towards food security. Marker-assisted backcrossing is one of the feasible methods to develop a new salt tolerant rice cultivar to cope with the challenge. The study was focused on to introgress salt tolerant genes from a tolerant rice line, FL-478 to Binadhan-7, an early, agronomically suitable and susceptible variety. Backcrossing was done during boro season; where Binadhan-7 was the recurrent parent and FL-478 was the donor parent. 141 BC1F1 lines were developed, which were subjected to foreground selection; the first level of selection of marker assisted backcrossing program. The aim of foreground selection was to identify the introgressed lines. 141 BC1F1 populations were evaluated with tightly linked salt tolerant markers; AP3206f, RM3412b and RM336. A total of 47 heterozygous BC1F1 lines were selected finally, which have alleles of both of the parents. Those introgressed lines could be efficiently used in further development of a stable early salt tolerant rice variety. DOI: http://dx.doi.org/10.3329/jbau.v11i1.18215 J. Bangladesh Agril. Univ. 11(1): 67-72, 2013

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.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

Quantitative trait locus for seizure susceptibility on mouse chromosome 5 confirmed with reciprocal congenic strains

2007 ◽  
Vol 31 (3) ◽  
pp. 458-462 ◽  
Author(s):  
Thomas N. Ferraro ◽  
George G. Smith ◽  
Candice L. Schwebel ◽  
Falk W. Lohoff ◽  
Patrick Furlong ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Genetic Background ◽  
Seizure Threshold ◽  
Maximal Electroshock ◽  
Seizure Susceptibility ◽  
Chromosome 5 ◽  
Congenic Strains ◽  
Combining Data ◽  
Trait Locus

Multiple quantitative trait locus (QTL) mapping studies designed to localize seizure susceptibility genes in C57BL/6 (B6, seizure resistant) and DBA/2 (D2, seizure susceptible) mice have detected a significant effect originating from midchromosome 5. To confirm the presence and refine the position of the chromosome 5 QTL for maximal electroshock seizure threshold (MEST), reciprocal congenic strains between B6 and D2 mice were created by a DNA marker-assisted backcross breeding strategy and studied with respect to changes in MEST. A genomic interval delimited by marker D5Mit75 (proximal to the acromere) and D5Mit403 (distal to the acromere) was introgressed for 10 generations. A set of chromosome 5 congenic strains produced by an independent laboratory was also studied. Comparison of MEST between congenic and control (parental genetic background) mice indicates that genes influencing this trait were captured in all strains. Thus, mice from strains having D2 alleles from chromosome 5 on a B6 genetic background exhibit significantly lower MEST compared with control littermates, whereas congenic mice harboring B6 chromosome 5 alleles on a D2 genetic background exhibit significantly higher MEST compared with control littermates. Combining data from all congenic strains, we conclude that the gene(s) underlying the chromosome 5 QTL for MEST resides in the interval between D5Mit108 (26 cM) and D5Mit278 (61 cM). Generation of interval-specific congenic strains from the primary congenic strains described here may be used to achieve high-resolution mapping of the chromosome 5 gene(s) that contributes to the large difference in seizure susceptibility between B6 and D2 mice.

scholarly journals Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 581-588
Author(s):  
Mohamed A F Noor ◽  
Aimee L Cunningham ◽  
John C Larkin
Keyword(s):  
Quantitative Trait Locus ◽  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Recombination Rate ◽  
Genome Project ◽  
Gene Density ◽  
Rate Variation ◽  
Trait Locus ◽  
Recombination Rate Variation

Abstract We examine the effect of variation in gene density per centimorgan on quantitative trait locus (QTL) mapping studies using data from the Drosophila melanogaster genome project and documented regional rates of recombination. There is tremendous variation in gene density per centimorgan across this genome, and we observe that this variation can cause systematic biases in QTL mapping studies. Specifically, in our simulated mapping experiments of 50 equal-effect QTL distributed randomly across the physical genome, very strong QTL are consistently detected near the centromeres of the two major autosomes, and few or no QTL are often detected on the X chromosome. This pattern persisted with varying heritability, marker density, QTL effect sizes, and transgressive segregation. Our results are consistent with empirical data collected from QTL mapping studies of this species and its close relatives, and they explain the “small X-effect” that has been documented in genetic studies of sexual isolation in the D. melanogaster group. Because of the biases resulting from recombination rate variation, results of QTL mapping studies should be taken as hypotheses to be tested by additional genetic methods, particularly in species for which detailed genetic and physical genome maps are not available.

Sign in / Sign up

Export Citation Format

Share Document