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.

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 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

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 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 Yield QTL analysis of Oryza sativa x O. glumaepatula introgression lines

2013 ◽  
Vol 48 (3) ◽  
pp. 280-286 ◽  
Author(s):  
Priscila Nascimento Rangel ◽  
Rosana Pereira Vianello ◽  
Arthur Tavares Oliveira Melo ◽  
Paulo Hideo Nakano Rangel ◽  
João Antônio Mendonça ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Interspecific Cross ◽  
Rice Genome ◽  
Introgression Lines ◽  
Wild Accession ◽  
Cultivated Rice ◽  
Two Generations ◽  
Ssr Loci ◽  
Donor Parent ◽  
Effect On Yield

The objective of this work was to evaluate the yield performance of two generations (BC2F2 and BC2F9) of introgression lines developed from the interspecific cross between Oryza sativa and O. glumaepatula, and to identify the SSR markers associated to yield. The wild accession RS‑16 (O. glumaepatula) was used as donor parent in the backcross with the high yielding cultivar Cica‑8 (O. sativa). A set of 114 BC2F1 introgression lines was genotyped with 141 polymorphic SSR loci distributed across the whole rice genome. Molecular analysis showed that in average 22% of the O. glumaepatula genome was introgressed into BC2F1 generation. Nine BC2F9 introgression lines had a significantly higher yield than the genitor Cica‑8, thus showing a positive genome interaction among cultivated rice and the wild O. glumaepatula. Seven QTL were identified in the overall BC2F2, with one marker interval (4879‑EST20) of great effect on yield. The alleles with positive effect on yield came from the cultivated parent Cica‑8.

scholarly journals Introgression of the Afila Gene into Climbing Garden Pea (Pisum sativum L.)

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1537
Author(s):  
Oscar Checa ◽  
Marino Rodriguez ◽  
Xingbo Wu ◽  
Matthew Blair
Keyword(s):  
Pisum Sativum ◽  
Production Costs ◽  
Yield Potential ◽  
Recurrent Parent ◽  
Linkage Drag ◽  
Progeny Testing ◽  
High Biomass ◽  
Garden Pea ◽  
Pisum Sativum L ◽  
Field Peas

The pea (Pisum sativum L.) is one of the most important crops in temperate agriculture around the world. In the tropics, highland production is also common with multiple harvests of nearly mature seeds from climbing plant types on trellises. While the leafless variant caused by the afila gene is widely used in developing row-cropped field peas in Europe, its use for trellised garden peas has not been reported. In this study we describe a pea breeding program for a high-elevation tropical environment in the Department of Nariño in Colombia, where over 16,000 hectares of the crop are produced. The most widespread climbing varieties in the region are ‘Andina’ and ‘Sindamanoy’, both of which have high-biomass architecture with abundant foliage. They are prone to many diseases, but preferred by farmers given their long production season. This plant type is expensive to trellis, with wooden posts and plastic strings used for vine staking constituting 52% of production costs. The afila trait could reduce these costs by creating interlocking plants as they do in field peas. Therefore, our goal for this research was to develop a rapid breeding method to introduce the recessive afila gene, which replaces leaves with tendrils, into the two commercial varieties used as recurrent parents (RPs) with three donor parents (DPs)—‘Dove’, ‘ILS3575′ and ‘ILS3568′—and to measure the effect on plant height (PH) and yield potential. Our hypothesis was that the afila gene would not cause linkage drag while obtaining a leafless climbing pea variety. Backcrossing was conducted without selfing for two generations and plants were selected to recover recurrent parent characteristics. Chi-square tests showed a ratio of 15 normal leaved to one afila leaved in the BC2F2 plants, and 31:1 in the BC3F2 generation. Selecting in the last of these generations permitted a discovery of tall climbing plants that were similar to those preferred commercially, but with the stable leafless afila. The method saved two seasons compared to the traditional method of progeny testing before each backcross cycle; the peas reached the BC2F2 generation in five seasons and the BC3F2 in seven seasons. This is advantageous with trellised peas that normally require half a year to reach maturity. Leafless garden peas containing the afila gene were of the same height as recurrent parents and, by the third backcross, were equally productive, without the high biomass found in the traditional donor varieties. The value of the afila gene and the direct backcrossing scheme is discussed in terms of garden pea improvement and crop breeding.

scholarly journals Recovery of Recurrent Parent Genome in a Marker-Assisted Backcrossing Against Rice Blast and Blight Infections Using Functional Markers and SSRs

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1411
Author(s):  
Samuel Chibuike Chukwu ◽  
Mohd Y. Rafii ◽  
Shairul Izan Ramlee ◽  
Siti Izera Ismail ◽  
Yusuff Oladosu ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Blast Resistance ◽  
Leaf Blight ◽  
Bacterial Leaf Blight ◽  
Functional Markers ◽  
Recurrent Parent ◽  
Selected Lines ◽  
Recurrent Parent Genome ◽  
Backcross Breeding ◽  
Marker Assisted Backcross Breeding

The most vital aspect of marker-assisted backcross breeding is the recurrent parent genome recovery. This enables the selection of only parents with recovered recipient/recurrent parent genome in addition to the targeted genes. The recurrent parent genome recovery (RPGR) ensures that non-desirable genomic segments are removed while the gene of interest is sustained in the recombined progenies without further segregations. This work was aimed at quantifying the RPGR of backcross populations with introgression of bacterial leaf blight resistance genes. Putra-1, a Malaysian elite variety, high yielding with inherent resistance to blast but susceptible to bacterial leaf blight (BLB), was crossed with IRBB60 which is resistant to BLB disease. The IRBB60 has four Xoo resistance genes—Xa4, xa5, xa13 and Xa21. Tightly linked polymorphic functional and SSR markers were used for foreground selection at every stage of backcrossing to select progenies with introgressed target genes. Background selection was done to quantify the percentage of RPGR in the selected lines using 79 confirmed polymorphic microsatellites. Result obtained showed that the percentage of RPGR was 80.11% at BC1F1, 95.30% at BC2F1 and 95.9% at BC2F2. The introgression of Xa4, xa5, xa13 and Xa21 Xoo resistance genes were faster through the adopted marker-assisted backcross breeding compared to what could be obtained through conventional breeding. All the 16 selected lines displayed resistance to BLB with three lines showing high resistance to the disease. The blast resistance contained in the genetic background of Putra-1 was also sustained in all the selected lines. The newly developed lines were recommended as new rice varieties for commercial cultivation.

Advanced backcross strategy for alien introgression for productivity enhancing traits in chickpea (Cicer arietinum L.)

2016 ◽  
Author(s):  
R. K. Bhavyasree ◽  
Sarvjeet Singh ◽  
Inderjit Singh
Keyword(s):  
Cicer Arietinum ◽  
Seed Yield ◽  
Growth Habit ◽  
Recurrent Parent ◽  
Linkage Drag ◽  
Seed Shape ◽  
Cicer Arietinum L ◽  
Advanced Backcross ◽  
Record Data ◽  
Prostrate Growth

A chickpea (Cicer arietinum L.) cultivar, GPF2, was crossed with two accessions, EC556270 and ILWC21, of its wild relative C. reticulatum with the objective to introgress productivity enhancing traits from wild to cultivated chickpea. The F1s were backcrossed to cultivated parent to generate backcross derived generations and also selfed to generate F3 progenies. In BC1F1 and BC2F1 generations, plants showing superiority for fruiting branches, pods and seed yield over the recurrent parent were recovered. A set of 77 BC1F2 and F3 progenies along with recurrent parent was grown to record data on various morphological traits, yield components and seed yield were recorded. There was significant improvement in number of pods, number of primary and secondary branches and seed yield. Some BC1F2 progenies recorded 30-32% higher seed yield as compared to recurrent parent. Many backcross progenies were superior to the cultivated parent for more than one trait. It was observed that F2 and F3 progenies were inferior as compared to the backcross derived progenies due to the undesirable characters like prostrate growth habit, seed shape and dull seed colour which were inherited from the wild parent. Results showed that the wild donors contributed several positive alleles for yield and yield contributing traits. The study also suggested that one or two backcrosses are required to reduce linkage drag of undesirable traits from the wild donors.

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

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Vivek Kumar Singh ◽  
Brahma Deo Singh ◽  
Amit Kumar ◽  
Sadhna Maurya ◽  
Subbaiyan Gopala Krishnan ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Rice Variety ◽  
Crop Improvement ◽  
Rice Cultivar ◽  
Seedling Stage ◽  
Basmati Rice ◽  
Recurrent Parent ◽  
Foreground Selection

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.

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