Theoretical determination of the optimum number of parents for synthetics

Summary From the consideration of the expressions of the mean and of the variances amongk-parent synthetics, it is possible, in the absence of epistasis, to give an algebraic determination of the optimum number of parents to include in a synthetic. The knowledge of four components of variance of inbred populations is necessary. Such components can be replaced by four simple statistics for the plant breeder: variances of general and specific combining abilities, variance among S₁ families from the parents, and covariance between S₁ value and general combining ability (GCA). A numerical study shows that this optimum is rather broad for a number of parents greater than four. As expected, the optimum tends to be higher for greater inbreeding depression. With inbreeding depression greater than 0.30, the maximum gain, in comparison to the random mating population with realistic selection intensity, would be less than 5%. In such a situation it will be better to use as synthetic the population improved by recurrent selection.     

Four rice QTL controlling number of spikelets per panicle expressed the characteristics of single Mendelian gene in near isogenic backgrounds

Development of quantitative trait loci (QTL) near isogenic lines is a crucial step to QTL isolation using the strategy of map-based cloning. In this study, a recombinant inbred line (RIL) population derived from two indica rice varieties, Zhenshan 97 and HR5, was employed to map QTL for spikelets per panicle (SPP). One major QTL (qSPP7) and three minor QTL (qSPP1, qSPP2 and qSPP3) were identified on chromosomes 7, 1, 2 and 3, respectively. Four sets of near isogenic lines (NILs) BC₄F₂ targeted for the four QTL were developed by following a standard procedure of consecutive backcross, respectively. These QTL were not only validated in corresponding NILs, but also explained amounts of phenotypic variation with much larger LOD scores compared with those identified in RILs. SPP in the four QTL-NILs expressed bimodal or discontinuous distributions and followed the expected segregation ratio of single Mendelian factor by progeny test. Finally, qSPP1, qSPP2, qSPP3 and qSPP7 were respectively mapped to a locus, 0.5 cM from MRG2746, 0.6 cM from MRG2762, 0.8 cM from RM49 and 0.7 cM from MRG4436, as co-dominant markers on the basis of progeny tests. These results indicate no matter how small effect minor QTL is, QTL may still express the characteristics of single Mendelian factor in NILs and isolation of minor QTL will be possible using high quality NILs. Pyramiding these QTL into a variety will largely enhance rice grain yield.     

Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice

In our previous studies, one putative QTL affecting number of spikelets per panicle (SPP) was identified in the pericentromeric region of rice chromosome 7 using a recombinant inbred population. In order to define the QTL (qSPP7), RI50, a recombinant inbred line with 70% of genetic background same as the female parent of Zhenshan 97, was selected to produce near-isogenic lines for the target region in the present study. In a BC₂F₂ population consisting of 190 plants, the frequency distribution of SPP was shown to be discontinuous and followed the expected Mendelian ratios (1:2:1 by progeny test) for single locus segregation. qSPP7 was mapped to a 0.4 cM region between SSR marker RM3859 and RFLP marker C39 based on tests of the BC₂F₂ population and its progeny. Its additive and dominant effects on SPP were 51.1 and 24.9 spikelets, respectively. Of great interest, the QTL region also had effects on grain yield per plant (YD), 1,000 grain weight (GW), tillers per plant (TPP) and seed setting ratio (SR). Significant correlations were observed between SPP and YD (r = 0.66) and between SPP and SR (r = −0.29) in the progeny test. 1082 extremely small panicle plants of a BC₃F₂ population containing 8,400 individuals were further used to fine map the QTL. It turns out that qSPP7 co-segregated with two markers, RM5436 and RM5499 spanning a physical distance of 912.4 kb. Overall results suggested that recombination suppression occurred in the region and positional cloning strategy is infeasible for qSPP7 isolation. The higher grain yield of Minghui 63 homozygote as compared to the heterozygote suggested that Minghui 63 homozygote at qSPP7 in hybrid rice could further improve its yield. Y. Z. Xing and W. J. Tang contributed equally to this work.     

The genetic origin of fragrance in NERICA1

In this study, we investigated the cause and origin of fragrance in NERICA1, a fragrant rice inbred line developed from an interspecific cross between two non-fragrant parents. The genetic cause of fragrance in NERICA1 was found to be due to a previously reported mutation in the BADH2 gene, the same allele responsible for the majority of modern fragrant rice varieties. Haplotype analysis around the BADH2 gene in NERICA1, its parents, and 95 other varieties carrying the badh2.1 allele identified the source of the badh2.1 allele in NERICA1 was a fragrant tropical japonica variety, WAB638-1, which had been growing in the vicinity of the NERICA1 nursery during varietal development. The allele-specific marker for the badh2.1 allele consistently predicted fragrance in the diverse African germplasm tested, making it very useful for marker-assisted breeding of fragrant rice varieties in Africa.     

Combining ability analysis over F1-F5 generations in diallel crosses of bread wheat

Summary Combining ability studies for grain yield and its primary component traits in diallel crosses involving seven diverse wheat cultivars of bread wheat (Triticum aestivum L.) over generations F₁-F₅ are reported. The general and specific combining ability variances were significant in all generations for all the traits except specific combining ability variance for number of spikes per plant in the F₅. The ratio of general to specific combining ability variances was significant for all the traits except grain yield in all the generations. This indicated an equal role of additive and non-additive gene effects in the inheritance of grain yield, and the predominance of the former for its component traits. The presence of significant specific combining ability variances in even the advanced generations may be the result of an additive x additive type of epistasis or evolutionary divergence among progenies in the same parental array. The relative breeding values of the parental varieties, as indicated by their general combining ability effects, did not vary much over the generations. The cheap and reliable procedure observed for making the choice of parents, selecting hybrids and predicting advanced generation (F₅) bulk hybrid performance was the determination of breeding values of the parents on the relative performance of their F₂ progeny bulks.     

Gene mutations in rye causing embryo lethality in hybrids with wheat: allelism and chromosomal localisation

In crosses between hexaploid wheat and inbred lines of rye, a small number of rye genotypes produce seeds carrying undifferentiated, non-viable embryos. Hybrids between such lines and those not showing this phenotype were used as pollen donors in crosses with bread wheat in order to determine the genetic basis of disturbed embryo development. A single gene, designated Eml-R1b, is causing this character. Molecular markers associated with F₂ genotypes derived from a contrasting rye inbred progeny were used for a linkage study. Recombinant inbred lines of an F₅ population served as testers. Eml-R1b maps to chromosome arm 6RL, along with two co-segregating microsatellite loci, Xgwm1103 and Xgwm732. Complementary interactions of deleterious genes in wheat and rye are discussed.     

Sex allocation variation in Daphnia pulex

Daphnia (Crustacea: Cladocera) reproduce by cyclical parthenogenesis in which the sex of offspring is environmentally determined. Although numerous studies have demonstrated that factors such as crowding and short-day photoperiod stimulate male production, there is limited information on variation in allocation to male and female offspring for any species of Daphnia . The present study assessed the presence or absence of male production in 96 isofemale lines (clones) from each of eight populations of Daphnia pulex . An average of 37% (range 18–51%) of clones failed to produce males under crowded conditions in the laboratory. A subset of 14 of these non-male-producing clones also failed to produce males under short-day photoperiod (8L:16D). Three male-producing clones were within-clone mated as well as crossed to three non-male-producing clones to study the inheritance of the failure to produce males. The average frequency of non-male-producing F ₁ progeny was significantly higher (58%, N = 486) among the outcrossed progeny than the inbred progeny (5%, N = 86). In addition, when sixteen of the male-producing outcrossed progeny were within-clone mated, only 7% ( N = 106) of the resulting F ₂ progeny failed to produce males. These results are consistent with a genetic basis for the absence of male production. Average survival of the progeny from the nine outcrossed matings was more than twice (67%) that of the inbred progeny from the three within-clone matings (30%), suggesting that within-clone mating would result in significant inbreeding depression. We present a model that suggests that even low levels of inbreeding could allow non-male-producing females to be maintained in a population. The co-occurrence of non-male-producing females and females that produce both males and females in Daphnia pulex bears a similarity to the gynodioecious breeding system found in some plant species.     

Genetics and ontogeny of alcohol dehydrogenase isozymes in the mouse: Evidence for a cis-acting regulator gene (Adt-1) controlling C2 isozyme expression in reproductive tissues and close linkage of Adh-3 and Adt-1 on chromsome 3

An electrophoretic variant previously reported for the stomach isozyme of alcohol dehydrogenase (ADH-C2) in inbred strains of Mus musculus (Holmes, 1977) has been used to localize the gene encoding this enzyme (Adh-3) on chromosome 3 near Va (varitint) (9.6 ± 3.6% recombinants). Genetic variation of ADH-C2 activity in male and female reproductive tissues among inbred strains and Harwell linkage testing stocks was also observed. Reproductive tissue ADH-C2 phenotypes were inherited in a normal Mendelian fashion among F₂ progeny of an F₁ (LII × C57BL/Go) × C57BL/Go backcross as though controlled by a single cis-acting regulator locus (designated Adt-1) with two alleles: Adt-1 ^a (presence of ADH-C2) and Adt-1 ^b (absence or low activity of ADH-C2). No recombinants were observed among 73 progeny or among 13 inbred strains and six Harwell linkage testing stocks of mice, indicating that Adh-3 and Adt-1 are closely linked or identical genes. A single recombinant phenotype was observed in Peru-Coppock mice, suggesting that they are separate genes. Ontogenetic analyses demonstrated that ADH-B₂ is present throughout development from late fetal stages in stomach, liver, and kidney; similar results were found for ADH-C2 in developing kidney and stomach extracts, whereas ADH-A2 exhibited high activity in liver extracts after 3 weeks of age in both sexes and in male kidney extracts after 6 weeks.     

Aflatoxin contamination in insect damaged seeds of horsegram under storage

Studies on one of the protein rich pulses, horsegram (Dolichos biflorus L.) were carried out to know how far these low risk pulses are free from aflatoxin contamination under severe insect infestation in storage. A total of 150 stored seed samples of horsegram were analyzed for the presence of aflatoxins by collecting 25 samples each of undamaged and insect damaged seeds of all the three varieties (PDM-1, PHG-1 and HG-96). More than 33% of insect damaged seed samples were contaminated with aflatoxin B₁ and B₂, whereas less than 8% of the undamaged seed samples contain only low levels of aflatoxin B₂. Higher levels of aflatoxin B₁ (up to 130 μg/kg) were reported in insect damaged seed samples of all the three varieties under study. The levels of aflatoxin B₂ were always lower than aflatoxin B₁ of the corresponding seed samples with insect damage. Aflatoxin B₁ was reported in both the undamaged and insect damaged seed samples of all the three varieties of horsegram. It is evident from the varietal response studies that PDM-1 and HG-96 varieties of horsegram are highly vulnerable to aflatoxin contamination whereas, PHG-1 variety is relatively less susceptible to it. In general, insect infestation leads to increase in fungal invasion (including aflatoxigenic fungi) and this further enhances the levels of aflatoxin contamination in horsegram seeds.     

Genetic factors affecting maize tolerance to low temperatures at emergence and germination

Summary On the basis of the percentage of plants emerging under laboratory cold-test conditions, inbred lines were divided into tolerant (T), semi-tolerant (I) and sensitive (S) to low temperatures. Tolerance to low temperature is, then, an inheritable and varietal plant characteristic.On average, local varieties showed the best emergence, followed by double crosses, single crosses and inbred lines in that order. Some tolerant hybrids and inbred lines had quite high emergence after 27 days at 6 °C. Thus the tolerant inbred lines Bc-130 E-5 and T-193/II had more emerged seeds (78 and 75% with embryo roots and 52 and 47% with stalk apices, respectively) with longer embryo roots and stalk apices than the sensitive inbred lines T-145/11 and W-8 at the end of this treatment.The two-year average emergence of 56 reciprocal single crosses and their parental inbred lines cold-tested at 6 °C and 8 °C indicates that the degree of tolerance to low temperatures is strongly dependent on the germination ability of the maternal parent of the cross, i. e. on maternal effect. The genetic mechanism of this inheritance is rather complex. The higher stand density of single crosses over inbred lines may be explained by complementary gene action in the seed embryo. The characteristics of the maternal parent were important in determining not only the percentage of germinated plants, but also the speed of germination and growth of the embryo root and stalk apex. With each parental inbred line the percentage emergence differed according to whether the line was used as the maternal or pollen parent in the crosses.     

Quantitative trait mapping in a diallel cross of recombinant inbred lines

A recombinant inbred intercross (RIX) is created by generating diallel F₁ progeny from one or more panels of recombinant inbred (RI) strains. This design was originally introduced to extend the power of small RI panels for the confirmation of quantitative trait loci (QTL) provisionally detected in a parental RI set. For example, the set of 13 C × B (C57BL/6ByJ × BALB/cByJ) RI strains can, in principle, be supplemented with 156 isogenic F₁s. We describe and test a method of analysis, based on a linear mixed model, that accounts for the correlation structure of RIX populations. This model suggests a novel permutation algorithm that is needed to obtain appropriate threshold values for genome-wide scans of an RIX population. Despite the combinational multiplication of unique genotypes that can be generated using an RIX design, the effective sample size of the RIX population is limited by the number of progenitor RI genomes that are combined. When using small RI panels such as the C × B there appears to be only modest advantage of the RIX design when compared with the original RI panel for detecting QTLs with additive effects. The RIX, however, does have an inherent ability to detect dominance effects, and, unlike RI strains, the RIX progeny are genetically reproducible but are not fully inbred, providing somewhat more natural genetic context. We suggest a breeding strategy, the balanced partial RIX, that balances the advantage of RI and RIX designs. This involves the use of a partial RIX population derived from a large RI panel in which the available information is maximized by minimizing correlations among RIX progeny.     

A PCR-based marker for a locus conferring aroma in vegetable soybean (<Emphasis Type="Italic">Glycine max</Emphasis> L.)

Vegetable soybean (Glycine max L.) is an important economic and nutritious crop in South and Southeast Asian countries and is increasingly grown in the Western Hemisphere. Aromatic vegetable soybean is a special group of soybean varieties that produce young pods containing a sweet aroma, which is produced mainly by the volatile compound 2-acetyl-1-pyrroline (2AP). Due to the aroma, the aromatic vegetable soybean commands higher market prices and gains wider acceptance from unfamiliar consumers. We have previously reported that the GmAMADH2 gene encodes an AMADH that regulates aroma (2AP) biosynthesis in soybeans (Arikit et al. 2010). A sequence variation involving a 2-bp deletion in exon 10 was found in this gene in all investigated aromatic varieties. In this study, a codominant PCR-based marker for the aroma trait in soybeans was designed based on the 2-bp deletion in GmAMADH2. The marker was verified in five aromatic and five non-aromatic varieties as well as in F₂ soybean population segregating for aroma. The aromatic genotype with the 2-bp deletion was completely associated with the five aromatic soybean varieties as well as the aromatic progeny of the F₂ population with seeds containing 2AP. Similarly, the non-aromatic genotype was associated with the five non-aromatic varieties and non-aromatic progeny. The perfect co-segregation of the marker genotypes and aroma phenotypes confirmed that the marker could be efficiently used for molecular breeding of soybeans for aroma.     

CROSSING-DISTANCE EFFECTS IN DELPHINIUM NELSONII: OUTBREEDING AND INBREEDING DEPRESSION IN PROGENY FITNESS

Depending on its genetic causes, outbreeding depression in quantitative characters may occur first in the free-living F₁ generation produced by a wide cross. In 1981–1985, we generated F₁ progenies by hand-pollinating larkspurs (Delphinium nelsonii) with pollen from 1-m, 3-m, 10-m, or 30-m distances. From the spatial genetic structure indicated by previous electrophoretic and reciprocal transplantation studies, we estimate that these crosses range from being inbred (f ≈ 0.06) to outbred. We planted 594 seeds from 66 maternal sibships under natural conditions. As of 1992, there was strong evidence for both inbreeding depression and outbreeding depression. Progeny from intermediate crossing distances grew approximately twice as large as more inbred or outbred progeny in the first 5 yr after planting (P = 0.013, repeated measures ANOVA), and survived almost 1 yr longer on average (contrast of 3-m and 10-m treatments versus 1 m and 30 m; P = 0.028, ANOVA). Twenty maternal sibships produced flowering individuals; only four and two of these represented 1-m and 30-m crossing distances, respectively (P = 0.021, G-test). The cumulative fitness of intermediate distance sibships averaged about twice that of 1-m sibships, and five to eight times that of 30-m sibships (P = 0.017, ANOVA). Thus, even though progeny of 1-m crosses were inbred to a degree only about one-eighth that of selling, inbreeding depression approximated 50%, and outbreeding depression equaled or exceeded 50% for all fitness components.     

The use of replicated progenies in marker-based mapping of QTL's

Summary Seven types of progeny are described which can be used in detection of linkage between marker loci and quantitative trait loci (QTL) in a cross between two inbred lines. Three types of progeny: recombinant inbred lines (RI); doubled haploid lines (DH); and S₁ lines can be used to detect linked main effects, d. DH and RI lines can be used to detect smaller effects than S₁ lines. However, S₁ lines can also be used to detect within-population dominance effects, h. The smallest d detectible is in the range of 1/2 to 1/12 the size of the corresponding LSD_(0.05) for the quantitative trait, using 100 lines and 6 replicates. The smallest h detectible is 3–4 times this size. Four types of progeny can be used to detect differences in the dominance behavior of alleles within the population relative to an allele in another inbred line (P₄: DH lines x P₄; RI lines x P₄; either F₂ x P₄ or S₁ lines x P₄; and progeny generated by crossing (F₁ x P₃) x P₄. Dominance differences in the range of 1 1/4 to 1/6 the size of the corresponding LSD_(0.05) are routinely detectible using 100 lines and 6 replicates. Increasing the numbers of progeny evaluated or the number of replicates allows for the detection of relatively smaller linked effects.Contribution of United AgriSeeds, Inc.     

Marker-based estimates of identity by descent and alikeness in state among maize inbreds

Molecular markers are useful for determining relationships and similarity among inbreds, especially if the proportion of marker loci with alleles common to inbreds i and j is partitioned into: (1) the probability that marker alleles are identical by descent (_Mf_ij); and (2) the conditional probability that marker alleles are alike in state, given that they are not identical by descent ( _ij). Our objectives were to: develop a method, based on tabular analysis of restriction fragment length polymorphism marker data, for estimating _Mf_ij, _ij, and the parental contribution to inbred progeny; validate the accuracy of the method with a simulated data set; and compare the pedigree-based coefficient of coancestry (f_ij) and _Mf_ij among a set of maize (Zea mays L.) inbreds. Banding patterns for 73 probeenzyme combinations were determined among 13 inbreds. Iterative estimation of _Mf_ij, _ij, and the parental contribution to progeny was performed with procedures similar to a tabular analysis of pedigree data. Deviations of _Mf_ij from pedigree-based f_ij ranged from 0.002 to 0.288, indicating large effects of selection and/or drift during inbreeding for some inbreds. Differences between marker-based estimates and expected values of parental contribution to inbred progeny were as large as 0.205. Results for a simulated set of inbreds indicated that tabular analysis of marker data provides more accurate estimates of _Mf_ij and _ij than other methods described in the literature. Tabular analysis requires the availability of marker data for all the progenitors of each inbred. When marker data are not available for the parents of a given inbred, _Mf_ij and _ij may still be calculated if parental contributions to the inbred are assumed equal to their expectations.     

Bu-1 andTh-1, two loci determining surface antigens of B or T lymphocytes in the chicken

Alloantisera were prepared by reciprocal immunizations with bursal or thymic lymphoid cells between chickens of two inbred lines identical at theB major histocompatibility locus. In cytotoxic assays, antibursa sera were specific for donor-line bursa cells without absorption; antithymus sera were similarly specific for donor-line thymus cells. Both types of sera cytolyzed some peripheral lymphoid cells from spleen, bone marrow, and blood. Absorption of either type of serum with peripheral blood leukocytes removed all cytotoxic reactivity for central lymphoid cells. The inheritance of the alloantigens detected by these specific antisera was studied in F₁, F₂, and backcross progeny from the two lines. Phenotypes were determined by a method in which antisera preabsorbed with progeny leukocytes were reacted against⁵¹Cr-labeled bursal or thymic cells from chickens of both lines. The results established two independent autosomal loci-Bu-1 andTh-1-determining antigens expressed, respectively, on bursal cells and peripheral B lymphocytes or on thymic cells and peripheral T lymphocytes. Cytotoxic testing of bursal or thymic cells from chickens of other inbred lines and F₁ populations led to the tentative conclusion that the number of alleles atBu-1 is restricted, whileTh-1 exhibits considerable multiple allelism.     

The expression and perpetuation of inherent somatic variation in regenerants from embryogenic cultures of Pennisetum glaucum (L.) R. Br. (pearl millet)

Summary Genetic analysis was conducted on the qualitative and quantitative traits of sexual progeny derived from embryogenic cultures of two inbred lines of Pennisetum glaucum (L.) R. Br. (pearl millet). These lines included a genetically stable inbred of Tift 23 BE and a genetic marker line, derived from Tift 23BE, which bore qualitative genetic markers for a dominant purple plant trait (P) and two recessive traits, early flowering (e₁) and yellow stripe (ys). Tissue culture regenerant populations (R₀) and progeny populations (R₁) produced from these plants by selfing showed no qualitative genetic variation when derived from the genetically stable inbred Tift 23BE. In contrast, stably inherited qualitative variation for a number of genetic markers was observed in R₀, R₁, and R₂ progeny of the genetic marker line. In a population of 1,911 plants regenerated over a 12-month period, 0.02% of the population lost or showed reduced expression of the purple plant trait and 92% of plants were chlorophyll deficient. Plants showing reduction or loss of anthocyanin synthesis also flowered later. None of the purple plants showed any significant variation in flowering time. The incidence of chlorophyll deficiency increased with time in culture, 51 % of the progeny regenerated after 1 month were chlorophyll deficient, while 100% of the plants regnerated after 12 months were chlorophyll deficient. Qualitative variation was also observed in control populations of the genetic marker line where 1 plant in a total of 1,010 lacked purple pigmentation and a total of 6% showed chlorophyll variation in the first generation (S₀). The presence of qualitative variation in controls suggests that the inherent variation present in the original explant was expressed and perpetuated in vitro. Quantitative variation was observed for a number of traits in the first sexual cycle (R₁) of the marker line but did not occur in a subsequent generation, suggesting that this variation was epigenetic.     

Association of AFLP markers with downy mildew resistance in autotetraploid alfalfa

The amplified fragment length polymorphism (AFLP) assay is an efficient method for the identification of molecular markers useful in the improvement of numerous crop species. The identification of AFLP markers linked to disease resistance genes has been shown in segregating populations from crosses of inbred lines. The development of inbred lines in alfalfa is not possible, but existing breeding programs have produced populations selected for resistance to a single pest. Two such populations, UC-123 and UC-143, differing only in selection for resistance to downy mildew (Peronospora trifoliorum de Bary) isolate I-8, were used in this study. Thirty-six resistant plants from UC-143, and 36 susceptible plants from UC-123 were screened for DNA polymorphisms using fourteen AFLP primer combinations. Four AFLP fragment markers, ACACTC₂₀₈, ACACTC₁₅₀, ACACAT₂₁₆ and ACACTC₄₈₆, were found to be significantly associated with disease susceptibility or resistance. Resistant and susceptible plants were crossed in a diallel scheme and the progeny were screened for resistance to P. trifoliorum isolate I8. Two of the AFLP markers, ACACTC₂₀₈ and ACACTC₄₈₆ were significantly associated with resistance in the F₁ and S₁ progeny. The utilization of two populations, comprised of 36 resistant and 36 susceptible plants, for the identification of DNA fragments associated with disease resistance proved successful. Seventy-two plants is a very manageable number and provides a starting point for further refinement of marker-trait associations.