Construction of three half-sib SSR linkage maps derived from overwintering cultivated rice and segregation distortion loci mapping

Segregation distortion is a common phenomenon that has been observed in genetics and plant breeding; however, the mechanism of segregation distortion is unknown. In the present study, three half-sib F2 populations derived from three japonica overwinter (perennial) rice varieties (W1, W2, and W3) crossed to the indica rice variety Minghui725 (MH725) were developed to construct three half-sib linkage maps. We established linkage map lengths of 2032.8, 2317.4, and 2108.7 cM with average intervals of 20.1, 20.5, and 19.7 cM using 101, 113, and 107 SSR markers in W1/MH725, W2/MH725, and W3/MH725, respectively. Discrepancies in marker order and genetic linkage distance occurred in the three half-sib linkage maps due to segregation distortion. A total of 88 markers exhibited segregation distortion across the three linkage maps at P < 0.01 level, 42 segregation distortion loci (SDLs) were detected across the three half-sib populations and exhibited variable LOD value that ranged from 3.2 (SDL2f) to 30.1 (SDL5d), and 13 of the 42 SDLs were repeatedly located at the same chromosomal regions of the previously published hybrid sterility quantitative trait loci. Data from this study provide an extensive archive for investigating the genetic characteristic of overwintering cultivated rice and the future exploration and innovation of overwintering rice breeding.

Apakah Saham Berlabel Syari’ah Memenuhi Kepatuhan dan Prinsip Moral Islam? (Study Kasus: Pasar Modal Syari’ah Indonesia)

The financial industry with the principle of shari'ah compliance has grown rapidly in almost all countries in recent years. Sharia Capital Market is an important segment of sharia financial development. The Islamic capital market must adhere to the moral principles of Islam, which are free from interest (riba), masyir (gambling) which automatically avoids things that lead to gharar (uncertainty). Islamic rules clearly forbid such conditions, so that the allocation of assets to Sharia stocks in the Islamic capital market tends to be bounded based on sharia moral principles. This study intends to evaluate the level of compliance of shariaa labeled stocks against bounded moral sharia. The method used is a measure of financial ratios based on POJK No. 35 /POJK.04/2017, linkage distance sharia compliance to default (DSCD) and the rate of compliance value for all shari'ah shares incorporated in the Indonesian Syari'ah Stock Index (ISSI). The fact is that not all shares with a syari'ah label are compliant with the existing Shari'ah moral principles.

Characterization of Induced Sugarcane Somaclones and their Sources Varieties Using Random Amplified Polymorphic DNA

Sugarcane somaclones and their sources varieties were analyzed by RAPD molecular markers to check the variation at molecular level based on 1.4% agarose gel electrophoresis (AGE). Six RAPD primers generated 237 bands with average 39.5 varied from 15 to 63 with size ranging 145 - 1000 bp among the four sugarcane varieties and their 12 somaclones. Genetic diversity or polymorphism information content (PIC) value ranged from 0.39 to 0.50 for all loci across the 4 varieties and their 12 somaclones based on RAPD markers. Dendrogram based on linkage distance using unweighted pair group method of arithmetic means (UPGMA) based on 6 RAPD primers indicated segregation of the 4 sugarcane varieties and their somaclones into two main clusters at linkage distance 36. Variety Isd 39 was observed in main cluster C1 while its (Isd 39) somaclones and other varieties (Isd 37, Isd 38 and Isd 40) and also their somaclones were found in main cluster C2 having different sub-clusters. Theirfore, it may be concluded that RAPD markers can be used for identification of somaclonal variation and the relationship between sources varieties and their somaclones.Plant Tissue Cult. & Biotech. 25(2): 223-229, 2015 (December)

GENETIC LINKAGE MAP FOR WATERMELON: SEGREGATION AND DISTRIBUTION OF DNA MARKERS

Genetic linkage map is being constructed for watermelon based on a testcross population and an F2 population. About 51.0% and 31.8% of the markers in the testcross and F2 populations are skewed form the expected segregation ratios. AFLP markers appeared to be clustered on linkage regions, while ISSR and RAPD markers are randomly dispersed on the genome. AFLP markers also have greater genetic distances as compared with ISSR and RAPD markers, resulting in significant increase of map distance. An initial genetic map (based on the testcross population) that contains 27 ISSR and 141 RAPD markers has a total linkage distance of 1,166.2 cM. The addition of 2 ISSR, 8 RAPD and 77 AFLP markers increased the genetic distance of the map to 2,509.9 cM. Similar results with AFLP markers were also shown in mapping experiments with an F2S7 recombinant inbred line (RIL) population that was recently constructed for watermelon. Although the skewed segregation, marker order appeared to be consistent in linkage groups of the testcross and the F2 population. Experiments with SSR, and EST markers are being conducted to saturate the linkage map of watermelon genome.

Exploring major gene-marker phase-typing strategies in marker-assisted selection schemes

Major gene-marker phase is generally assumed to be family specific. This has the consequence in relation to marker-assisted selection (MAS) that phase information about each family may need to be collected through progeny testing, which could represent a substantial cost. This paper examines the effect of different policies in relation to major gene-marker phase-typing on response to MAS. The different policies considered varied in the criteria by which individuals were selected for phase-typing, the number of individuals phase-typed, and the frequency of establishing phase. Stochastic simulation of a closed breeding nucleus, with either high or low levels of inbreeding and undergoing selection for two traits, was utilized. Total response under MAS was lower than that under genotypic assisted selection (GAS) for all phase-typing policies. For example, additional gains of 70% under GAS, achieved in year 1 and in comparison with non-MAS, corresponded to additional gains of 43% and 15% under MAS for linkage distances of 1 cM and 20 cM, respectively. The different phase-typing policies examined in relation to MAS did not have any effect on total response, although there were small effects on major gene response. For breeding nuclei with either level of inbreeding, higher major gene response was achieved when phase-typed sires were selected on the basis of high ranking for genetic merit rather than connectivity to the other selection candidates. Further, increasing the number of males phase-typed within any year did not increase the rate of major gene response, although phase-typing in more years was favourable for the large linkage distance. An overall conclusion of this study is that additional gain could be achieved under MAS within a closed nucleus when progeny testing to determine major gene-marker phase was limited to from one to a few individuals.

Inheritance of Reverse Margo Seedcoat Pattern and Allelism between the Genes J for Seedcoat Color and L for Partly Colored Seedcoat Pattern in Common Bean

Two common bean (Phaseolus vulgaris L.) genes, J (modifies seedcoat color and pattern) and L (modifies partly colored seedcoat pattern), were tested for allelism using genetic tester stocks. Those stocks have a common genetic background by backcrossing to the recurrent parent, Florida dry bean breeding line 5-593, that has black self-colored seeds and purple flowers due to the genotype T P [C r] Z J G B V Rk. Specifically, the L gene from `Thuringia' and the lers gene from `Early Wax' were tested for allelism with the j gene from various genetic tester stocks. L was found to be identical with j, but lers was a different allele at J. We propose the gene symbols J (formerly l), j (formerly L), and jers (formerly lers). The seedcoat genotype of `Thuringia' was found to be t P C z j g b vlae rkd. A new seedcoat pattern called reverse margo was found to be determined by the genotype T/t z/z j/jers in a P C G B V genetic background. A randomly amplified polymorphic DNA marker was developed for the j gene (formerly L) from `Thuringia' using bulk segregant analysis in an F2 population segregating for j vs. J in a t z genetic background, i.e., from the cross t z j × t z J in BC1 to 5-593. The linkage distance between marker OL4525 and j was determined to be 1.2 cM. In a population segregating for J and jers, the distance between the marker and jers was determined to be 4.7 cM. The utility of marker OL4525 is limited primarily to the Middle American gene pool.

A Genetic Linkage Map for Watermelon Based on Randomly Amplified Polymorphic DNA Markers

A genetic linkage [randomly amplified polymorphic DNA (RAPD)-based] map was constructed for watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] using a BC1 population [PI 296341-fusarium wilt resistant × New Hampshire Midget (fusarium susceptible)] × `New Hampshire Midget'. The map contains 155 RAPD markers, and a 700-base pair sequenced characterized amplified region (SCAR) marker that corresponds to a fragment produced by the RAPD primer GTAGCACTCC. This marker was reported previously as linked (1.6 cM) to race 1 fusarium wilt resistance in watermelon. The markers segregated to 17 linkage groups. Of these, 10 groups included nine to 19 markers, and seven groups included two to four markers. The map covers a genetic linkage distance of 1295 cM. Nine of the 10 large linkage groups contained segments with low (or no) level of recombination (0 to 2.6 cM) among markers, indicating that the watermelon genome may contain large chromosomal regions that are deficient in recombination events. The map should be useful for identification of markers linked closely to genes that control fruit quality and fusarium wilt (races 1 and 2) resistance in watermelon.

Inheritance and Linkage Relationships of Melon (Cucumis melo L.) Isozymes

Nineteen polymorphic and eleven monomorphic isozyme loci were identified in thirteen enzyme systems in a survey of four-hundred melon (Cucumis melo L.) accessions. Segregation of allozymes in F2 and backcross (BC) families for isozyme loci agreed with the expected 1:2:1 and 1:1 segregation ratios (P <0.01). Eleven isozyme loci were linked and were integrated to form a map containing two linkage groups spanning 98 cM with a mean linkage distance of ≈9 cM. Linkage groups (A and B) contain the following loci in the order: A Fdp-2, Pgd, Pgm, Mpi-1, Idh, and Ac, and B Pep-gl, Mdh-2, Mdh-4, Mdh-5, Mdh-6. The remaining eight loci (Acp-1, Acp-4, Ak-4, Fdp-1, Gpi, Mpi-2, Pep-la, and Pep-pap) segregated independently. The isozyme map constructed in this study provides genomic information for future linkage studies with economically important traits and concensus map construction through map merging.

Inheritance and Linkage Analysis of a Blotchy Root Pigment Phenotype in Red Beet

The primary pigments in red beet are the betalains, which include the red-violet betacyanins and the yellow betaxanthins. The recent adoption of betalain pigments from red beet as an alternative to synthetic food dyes has heightened interest in genetic modification of pigment production. Dominant alleles at two tightly-linked loci (R and Y) condition production of betalain pigment in the beet plant; however, several alleles at the R locus influence pigment amount and distribution. A mutant phenotype, characterized by irregular sectors of blotchy red and white root color, arose spontaneously in the beet breeding nursery. The blotchy mutant plant was used in crosses with non-blotchy inbred lines to characterize its inheritance. Chisquare goodness-of-fi t tests of segregation data in backcross and F2 generations for several genetic backgrounds did not deviate from the hypothesis that a single recessive gene controls the blotchy phenotype. Linkage analysis was conducted to determine if the blotchy phenotype was conditioned by a new locus or an allele at a previously described locus. Our data indicate the bl gene resides at a newly described locus linked to R and Y. Maximum likelihood estimation revealed a linkage distance between R and Y of 8.95 ± 0.49 cM. The linkage distance between R and BL was calculated at 13.99 ± 1.18 cM, and the overall linkage between Y and BL was determined to be 28.8 ± 4.2 cM. Our data suggest the RYBL genomic region plays a critical role in the genetic control of betalain biosynthesis.