Identification of stably expressed QTL for heading date using reciprocal introgression line and recombinant inbred line populations in rice

SummaryTwo sets of reciprocal introgression lines (ILs) and a population of recombinant inbred lines (RILs) derived from the cross between japonica cultivar Xiushui09 and indica breeding line IR2061-520-6-9 (abbreviated as IR2061) were used to identify QTL for heading date (HD). Phenotyping was conducted in Hainan Island for two winter seasons (2007 and 2009). Nine QTLs were detected in the ILs with Xiushui09 background (XS-ILs), and four of which were repeatedly mapped across 2 years. Five QTLs were identified in the ILs with IR2061 background (IR-ILs), and three of which were commonly detected in 2 years. All commonly detected QTL had the same direction of gene effect. Seven QTL for HD were identified in the RILs in 2009. Only three (25%) QTLs were commonly detected using all the three populations (XS-ILs, IR-ILs and RILs). The number of commonly identified QTLs among populations was related to degree of similarity of their genetic backgrounds, suggesting that the genetic background effect is important for detecting HD QTL. QHd7 and QHd10b stably expressed in different populations and across years thus would be exploited in rice breeding programme. Moreover, lines with both of QHd7 and QHd10b resulted in at least 3 days earlier than lines with only one of them QTL, showing evident pyramiding effect.

Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice

Effect of genetic background on detection of quantitative trait locus (QTL) governing salinity tolerance (ST) was studied using two sets of reciprocal introgression lines (ILs) derived from a cross between a moderately salinity tolerant japonica variety, Xiushui09 from China, and a drought tolerant but salinity susceptible indica breeding line, IR2061–520–6-9 from the Philippines. Salt toxicity symptoms (SST) on leaves, days to seedling survival (DSS), and sodium and potassium uptake by shoots were measured under salinity stress of 140 mmol/L of NaCl. A total of 47 QTLs, including 26 main-effect QTLs (M-QTLs) and 21 epistatic QTLs (E-QTLs), were identified from the two sets of reciprocal ILs. Among the 26 M-QTLs, only four (15.4%) were shared in the reciprocal backgrounds while no shared E-QTLs were detected, indicating that ST QTLs, especially E-QTLs, were very specific to the genetic background. Further, 78.6% of the M-QTLs for SST and DSS identified in the reciprocal ILs were also detected in the recombinant inbred lines (RILs) from the same cross, which clearly brings out the background effect on ST QTL detection and its utilization in ST breeding. The detection of ILs with various levels of pyramiding of nonallelic M-QTL alleles for ST from Xiushui09 into IR2061-520-6-9 allowed us to further improve the ST in rice.

The Genetic Background Effect on Domesticated Species: A Mouse Evolutionary Perspective

Laboratory mouse strains are known for their large phenotypic diversity and serve as a primary mammalian model in genotype-phenotype association studies. One possible attempt to understand the reason for this diversity could be addressed by careful investigation of the unique evolutionary history of their wild-derived founders and the consequence that it may have on the genetic makeup of the laboratory mouse strains during the history of human fancy breeding. This review will summarize recently published literature that endeavors to unravel the genetic background of laboratory mouse strains, as well as give new insights into novel evolutionary approaches. I will explain basic concepts of molecular evolution and the reason why it is important in order to infer function even among closely related wild and domesticated species. I will also discuss future frontiers in the field and how newly emerging sequencing technologies could help us to better understand the relationship between genotype and phenotype.

A Single Gene Cluster Controls Incompatibility and Partial Resistance to Various Melampsora larici-populina Races in Hybrid Poplars

Complete cosegregation for race-specific incompatibility with three Melampsora larici-populina rust races was observed in five F1 hybrid progenies of Populus, with different patterns among the various progenies. A single gene cluster could explain these segregations: one locus with multiple alleles or two tightly linked loci controlling complete resistance to E1 and E3, and two tightly linked loci for E2. The random amplified polymorphic DNA marker OPM03/04_480 was linked to that cluster in all families (<1 cM). This marker accounted for more than 70% of the genetic variation for field resistance in each family (heritability ≈ 0.40). The same marker accounted for up to 64% of the clonal variation for growth in the nursery under natural inoculum pressure; the weak tolerance to rust of F1 interspecific hybrids was attributed to a genetic background effect. Partial resistance was split into epidemiological components (heritability ranged from 0.35 to 0.87). Genotypic correlations among resistance traits for the different races were high (0.73 to 0.90). However, correlations among different resistance components for a single race were not all significant. A major quantitative trait locus for all components of partial resistance to E2 was associated to the cluster controlling incompatibility to E1 and E3 and marked by OPM03/04_480 (R2from 48 to 68%).