Recombinant Inbreeding Research Articles

Recombination Hotspots in Soybean [Glycine Max (L.) Merr.

Recombination allows for the exchange of genetic material between two parents which plant breeders exploit to make improved cultivars. This recombination is not distributed evenly across the chromosome. Recombination mostly occurs in euchromatic regions of the genome and even then, recombination is focused into clusters of crossovers termed recombination hotspots. Understanding the distribution of these hotspots along with the sequence motifs associated with them may lead to methods that enable breeders to better exploit recombination in breeding. To map recombination hotspots and identify sequence motifs associated with hotspots in soybean [Glycine max (L.) Merr.], two bi-parental recombinant inbred lines populations were genotyped with the SoySNP50k Illumina Infinium assay. A total of 451 recombination hotspots were identified in the two populations. Despite being half-sib populations, only 18 hotspots were in common between the two populations. While pericentromeric regions did exhibit extreme suppression of recombination, twenty-seven percent of the detected hotspots were located in the pericentromeric regions of the chromosomes. Two genomic motifs associated with hotspots are similar to human, dog, rice, wheat, drosophila, and arabidopsis. These motifs were a CCN repeat motif and a poly-A motif. Genomic regions spanning other hotspots were significantly enriched with the tourist family of mini-inverted-repeat transposable elements that resides in less than 0.34% of the soybean genome. The characterization of recombination hotspots in these two large soybean bi-parental populations demonstrates that hotspots do occur throughout the soybean genome and are enriched for specific motifs but their locations may not be conserved between different populations.

Fine mapping of a panicle blast resistance gene Pb-bd1 in Japonica landrace Bodao and its application in rice breeding

BackgroundRice blast caused by Magnaporthe oryzae is the most devastating disease in rice production. Compared with seedling blast, panicle blast is considered to be more destructive, which can occur without being preceded by severe seedling blast. However, panicle blast resistance research is rarely reported.ResultsBodao, a japonica landrace from Taihu Lake region, showed a high level of panicle blast resistance. In this study, a mapping population of 212 recombination inbreeding lines (RILs) was developed from a cross of Bodao and the susceptible cultivar Suyunuo, and the RILs were evaluated for panicle blast resistance in three trials. Two quantitative trait loci (QTLs) qPb11–1 and qPb6–1 for panicle-blast resistance were identified, including a major QTL qPb11–1 (Pb-bd1) on chromosome 11 of Bodao explaining from 55.31% to 71.68% of the phenotype variance, and a minor QTL qPb6–1 on chromosome 6 of Suyunuo explaining from 3.54% to 6.98% of the phenotype variance. With the various segregation populations, Pb-bd1 was fine mapped in a 40.6 Kb region flanked by markers BS83 and BS98, and six candidate genes were identified within this region, including one gene encoding NAC domain-containing protein, one gene encoding unknown expression proteins, two genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) type disease resistance proteins, and two genes encoding von Willebrand factor type A (VWA) domain containing proteins. For application in rice breeding, three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by using molecular assisted method (MAS) from the commercial variety Nanjing46 (NJ46).ConclusionTwo QTLs, qPb11–1(Pb-bd1) and qPb6–1 conferring panicle blast resistance, were identified from japonica landrace Bodao and Suyunuo.qPb11–1(Pb-bd1) was fine mapped in a 40.6 Kb region flanked by marker BS83 and BS98. Three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by MAS method from the commercial variety NJ46. It indicated that Pb-bd1 would be useful gene source in panicle blast resistance breeding.

QTL analysis for cold tolerance at seedling stage using Hanareum2/Unkwang recombinant inbreeding lines in rice

Tae-Heon Kim1, Ji-Yoon Lee1, Su-Min Jo1, Jun-Hyun Cho1, Jong-Hee Lee2, You-Chun Song1, Dong-Soo Park1, Myung-Kyu Oh1, Dongjin Shin1*. Korean J. Breed. Sci. 2017;49:334-43. https://doi.org/10.9787/KJBS.2017.49.4.334

Characterization and Fine Mapping of a Blast Resistant Gene Pi-jnw1 from the japonica Rice Landrace Jiangnanwan.

Rice blast is a destructive disease caused by Magnaporthe oryzae, and it has a large impact on rice production worldwide. Compared with leaf blast resistance, our understanding of panicle blast resistance is limited. The japonica landrace Jiangnanwan from Taihu Lake region in China shows highly resistance to panicle and leaf blast. In this study, three generations (F2:5, F2:6, F2:7) consisting of 221 RILs (recombination inbreeding lines), developed from the cross of Jiangnanwan and Suyunuo, a susceptible-blast japonica variety, were evaluated for panicle blast resistance in the fields and leaf blast resistance in greenhouse in Nanjing in 2013, 2014 and 2015. A blast resistance gene Pi-jnw1 referring to panicle blast resistance and leaf blast resistance was identified in the three generations and located in the region of RM27273 and RM27381 in chromosome 11. The RIL18 line harboring Pi-jnw1 was selected to be backcrossed with Suyunuo to develop BC2F2 populations. According to the genotyping of 1,150 BC2F2 individuals and panicle blast and leaf blast resistance evaluation of 47 recombinants between RM27150 and RM27381, Pi-jnw1 was finally mapped to the 282 kb region between markers W28 and BS39. This study revealed that Jiangnanwan harboring a panicle blast and leaf blast resistance gene Pi-jnw1 could be a genetic source for breeding new rice cultivars with panicle blast resistance.

QTL mapping of panicle blast resistance in japonica landrace heikezijing and its application in rice breeding

The rice blast caused by Magnaporthe oryzae is one of the most devastating diseases worldwide, and the panicle blast could result in more loss of yield in rice production. However, the quantitative trait loci (QTLs) and genes related to panicle-blast resistance have not been well studied due to the time-consuming screening methodology involved and variation in symptoms. The QTLs for panicle blast resistance have been mapped in a population of 162 RILs (recombination inbreeding lines), derived from a cross between a highly blast-resistant rice landrace, Heikezijing, and a susceptible variety, Suyunuo. Two QTLs for panicle-blast resistance, qPbh-11–1 and qPbh-7-1, were identified, which were distributed on chromosomes 11 and 7. The QTL qPbh-11–1 was stably detected in three independent experiments, at Nanjing in 2013 and 2014 and at Hainan in 2014, located between the region of RM27187 and RM27381 on the distal end of chromosome 11 far from the reported resistant loci Pb1 and qPbm11 for panicle blast. The QTL qPbh-7-1 was detected only at Nanjing in 2013 and located between the region of M18 and RM3555 on chromosome 7. With marker-assisted selection (MAS) three introgression lines with the major panicle blast-resistance QTL qPbh-11–1 were developed from a recurrent parent Nanjing 44 (NJ44) and the panicle resistance of introgression lines was improved 46.36–55.47 % more than NJ44. Based on the results provided, Heikezijing appears to be a valuable source for panicle blast resistance.

Statistical method for mapping QTLs for complex traits based on two backcross populations

Most important agronomic and quality traits of crops are quantitative in nature. The genetic variations in such traits are usually controlled by sets of genes called quantitative trait loci (QTLs), and the interactions between QTLs and the environment. It is crucial to understand the genetic architecture of complex traits to design efficient strategies for plant breeding. In the present study, a new experimental design and the corresponding statistical method are presented for QTL mapping. The proposed mapping population is composed of double backcross populations derived from backcrossing both homozygous parents to DH (double haploid) or RI (recombinant inbreeding) lines separately. Such an immortal mapping population allows for across-environment replications, and can be used to estimate dominance effects, epistatic effects, and QTL-environment interactions, remedying the drawbacks of a single backcross population. In this method, the mixed linear model approach is used to estimate the positions of QTLs and their various effects including the QTL additive, dominance, and epistatic effects, and QTL-environment interaction effects (QE). Monte Carlo simulations were conducted to investigate the performance of the proposed method and to assess the accuracy and efficiency of its estimations. The results showed that the proposed method could estimate the positions and the genetic effects of QTLs with high efficiency.

Shortened conditioned eyeblink response latency in male but not female Wistar-Kyoto hyperactive rats.

Reductions in the volume of the cerebellum and impairments in cerebellar-dependent eyeblink conditioning have been observed in attention-deficit/hyperactivity disorder (ADHD). Recently, it was reported that subjects with ADHD as well as male spontaneously hypertensive rats (SHR), a strain that is frequently employed as an animal model in the study of ADHD, exhibit a parallel pattern of timing deficits in eyeblink conditioning. One criticism that has been posed regarding the validity of the SHR strain as an animal model for the study of ADHD is that SHRs are not only hyperactive but also hypertensive. It is conceivable that many of the behavioral characteristics seen in SHRs that seem to parallel the behavioral symptoms of ADHD are not solely due to hyperactivity but instead are the net outcome of the interaction between hyperactivity and hypertension. We used Wistar-Kyoto Hyperactive (WKHA) and Wistar-Kyoto Hypertensive (WKHT) rats (males and females), strains generated from recombinant inbreeding of SHRs and their progenitor strain, Wistar-Kyoto (WKY) rats, to compare eyeblink conditioning in strains that are exclusively hyperactive or hypertensive. We used a long-delay eyeblink conditioning task in which a tone conditioned stimulus was paired with a periorbital stimulation unconditioned stimulus (750-ms delay paradigm). Our results showed that WKHA and WKHT rats exhibited similar rates of conditioned response (CR) acquisition. However, WKHA males displayed shortened CR latencies (early onset and peak latency) in comparison to WKHT males. In contrast, female WKHAs and WKHTs did not differ. In subsequent extinction training, WKHA rats extinguished at similar rates in comparison to WKHT rats. The current results support the hypothesis of a relationship between cerebellar abnormalities and ADHD in an animal model of ADHD-like symptoms that does not also exhibit hypertension, and suggest that cerebellar-related timing deficits are specific to males.

Uses of Forward and Reverse Genetics in Mice to Study Gene Function

As the focus of human genetics shifts from Mendelian traits to complex diseases, a sophisticated genetic tool kit-with space for genetics (classical, molecular, statistical, and quantitative), metabolics, proteomics, bioinformatics, and mathematics-is required to elucidate their multifactorial traits and regulatory processes. Importantly, mouse resources optimized to study the actions of isolated genetic loci on a fixed background are insufficient on their own for studying intact polygenic networks and genetic interactions, and researchers must work in the context of experimental model systems that optimally mimic the genetic structure of human populations. The success of such phenogenomic approaches depend on the efficacy by which specific mutations (gene targeting) and variability (recombinant inbreeding) can be introduced into the mouse genome, and on the optimization of phenotyping analyses of the mutant mouse lines. This unit describes the basic genetic approaches used to in the study of mouse model systems.

Recombinant inbreeding in mice reveals thresholds in embryonic corpus callosum development

The inbred strains BALB/cWah1 and 129P1/ReJ both show incomplete penetrance for absent corpus callosum (CC); about 14% of adult mice have no CC at all. Their F(1) hybrid offspring are normal, which proves that the strains differ at two or more loci pertinent to absent CC. Twenty-three recombinant inbred lines were bred from the F(2) cross of BALB/c and 129, and several of these expressed a novel and severe phenotype after only three or four generations of inbreeding - total absence of the CC and severe reduction of the hippocampal commissure (HC) in every adult animal. As inbreeding progressed, intermediate sizes of the CC and the HC remained quite rare. This striking phenotypic distribution in adults arose from developmental thresholds in the embryo. CC axons normally cross to the opposite hemisphere via a tissue bridge in the septal region at midline, where the HC forms before CC axons arrive. The primary defect in callosal agenesis in the BALB/c and 129 strains is severe retardation of fusion of the hemispheres in the septal region, and failure to form a CC is secondary to this defect. The putative CC axons arrive at midline at the correct time and place in all groups, but in certain genotypes, the bridge is not yet present. The relative timing of axon growth and delay of the septal bridge create a narrow critical period for forming a normal brain.

Dissociation of genetic hyperactivity and hypertension in SHR.

The Wistar Kyoto strain of spontaneously hypertensive rat (SHR) has been characterized as behaviorally hyperactive as well as hypertensive. The relationship between these two inbred traits remains uncertain, and their coexistence in the SHR has complicated studies of central nervous system mechanisms underlying the hypertensive process. A breeding program was initiated to examine the possible genetic linkage of these two traits which, if separable, would allow us to develop substrains of SHR that are hypertensive without being hyperactive, or hyperactive without being hypertensive. We crossed SHR males with Wistar Kyoto, normotensive (WKY) female rats and produced F1 hybrids which were then randomly inbred to produce an F2 population. When tested at 12 weeks of age, F2 rats exhibited the expected wide range of mean systolic blood pressures (BP), from 111 to 174 mm Hg, as determined using indirect tail plethysmography. The BP in the parental rats at the time of breeding (16 weeks) was 187 +/- 4.5 mm Hg (SHR males, n = 7) and 111 +/- 2.4 (WKY females, n = 7). Locomotor activity was determined in an automated activity cage in F1 and F2 rats at 12 weeks of age. These strains exhibited a wide range of phenotypic distribution of locomotor activity scores, and the mean scores were intermediary between those of SHR rats and WKY rats of the same age. Among individual rats of both the F1 and F2 hybrid strains, there was no correlation between the activity score and the level of the BP at 12 weeks of age. These findings indicated that the genes responsible for the hypertensive trait and those responsible for the hyperactivity trait were not tightly linked in the hybrid populations, suggesting that different genetic factors were involved in the transmission of each of these traits. Accordingly, it should be possible to separate the two traits by further selective, recombinant inbreeding procedures.