QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.

Genetic Diversity of Maize Populations Developed by Two Kinds of Recurrent Selection Methods Investigated with SSR Markers

Two cycles of biparental mass selection （MS） and one cycle of half-sib-S3 family combining selection （HS-S3） for yield were carried out in 2 synthetic maize populations P4C0 and P5C0 synchronously. The genetic diversity of 8 maize populations, including both the basic populations and their developed populations, were evaluated by 30 SSR primers. On the 30 SSR loci, a total of 184 alleles had been detected in these populations. At each locus, the number of alleles varied from 2 to 14, with an average of 6.13. The number and ratio of polymorphic loci in both the basic populations were higher than those of their developed populations, respectively. There was nearly no difference after MS but decreased after HS-S3 in both the basic populations in the mean gene heterozygosity. The mean genetic distance changed slightly after MS but decreased in a bigger degree after HS-S3 in both the basic populations. Analyses on the distribution of genetic distances showed that the ranges of the genetic distance were wider after MS and most of the genetic distances in populations developed by HS-S3 were smaller than those in both the basic populations. The number of genotypes increased after MS but decreased after HS-S3 in both the basic populations. The genetic diversity of intra-population was much more than genetic diversity of inter-population in both the basic populations. All these indexes demonstrated that the genetic diversity of populations after MS was similar to their basic populations, and the genetic diversity was maintained during MS, whereas the genetic diversity of populations decreased after HS-S3. This result indicated that heterogeneity between some of the individuals in the developed populations increased after MS, whereas the populations become more homozygotic after HS-S3.

Incubation strategies of the Black-necked Crane(Grus nigricollis) in relation to ambient temperature and time of day

Background: The behavior of cranes reflects many of their survival strategies, but little has been known of the incubation strategies of cranes, in which both parents share incubation duties, in response to cold temperatures in alpine environments. The lack of information may restrict the effective conservation of the threatened Black-necked Crane(Grus nigricollis), a biparental bird nesting in high elevation wetlands.Methods: We directly observed and used infrared video cameras from 2014 to 2015 to study the incubation behavior and quantitatively measured the frequency and details of egg turning behavior in the Black-necked Crane at the Yanchiwan National Nature Reserve in western Gansu Province, China.Results: At lower ambient temperatures in the morning, crane parents spent more time on the nest with less recess frequency and prolonged on-bout duration, while at higher temperatures around noon, the parents had more frequent recesses from incubation and shorter periods between nest exchanges. They adjusted the amount of time incubating by varying the recess frequency and the length of on-bout duration. Mean nest attendance and egg turning frequency of females were significantly higher than those of the males. The nest attendance and on-bout duration of females showed a significantly negative relationship with those of males. The two parents responded differently to the change of temperature. Females spent more time on the nest at lower morning temperatures, while males increased their time on the nest at higher temperatures after noon. Higher incubation recess frequency and egg turning frequency were observed at noon, probably because parents spent more time foraging, taking advantage of the lower egg cooling rate.Conclusion: Both Black-necked Crane parents in the alpine environment adjusted their behavior in response to the thermal requirements of eggs and the weather conditions experienced. Our findings demonstrate that parents of this species incubated in different but complementary ways and efficiently enhanced egg care in a dynamic environment, so as to maximize benefits from the warm portion of the day and the intense solar radiation while minimizing the cost of rewarming eggs and the risks of cooling eggs.

Effect of mate size on maternal reproductive effort in the convict cichlid Amatitlania siquia

The differential allocation hypothesis predicts individuals will increase their reproductive investment when mated to a high quality partner. In many species of fish with biparental care females prefer large males due to the males＇ greater ability to raise more offspring to independence. I examined the relationship between mate quality, parental care and number of offspring in a natural population of convict cichlids Amatitlania siquia. The frequency of frontal displays by females was positively correlated with male standard length. Additionally, as males increased in length relative to their mate, females increased the frequency of chases towards predators, while males decreased the number of displays towards brood predators. This trade-off in parental effort within a pair due to mate quality is a key prediction of differential allocation. The number of offspring was correlated with male, but not female, standard length. These results support the differential allocation hypothesis in that females offered more parental care to offspring of a larger male, while their mates decreased the amount of care they provided. AdditionaUy, females benefited in terms of number of offspring by pairing with higher quality mates. Increased female investment may provide an incentive to ensure male care and maintain pair bonding, which could lead to greater reproductive success through increased offspring sur- vival [Current Zoology 58 （1）： 66-72, 2012].

Do females influence paternal responsiveness in male prairie voles Microtus ochrogaster by increasing the salience of infant odors？

Male prairie voles become more responsive to infants following cohabitation with a female. Exposure to female sen- sory cues prior to offspring birth may influence male paternal tendencies by modifying his response to infant odors in particular or to odors in general. To test these hypotheses, males were housed with an unfamiliar female or a same-sex sibling for 13 days then examined for their response towards either live infants or infant-like inanimate objects covered with one of three odors： wa- ter, infant, sub-adult. We recorded the number of males that retrieved and manipulated the infants or odor-covered objects and measured the frequency and duration of time males spent attending to them or engaged in other non-social activities. Fe- male-Cohabited males approached the container holding infant-odor covered objects faster than Male-Cohabited males, but showed no differences in time spent manipulating those objects. Males in both groups spent more time manipulating live infants than odor-covered objects. However, Female-Cohabited subjects were more likely to manipulate odor-covered objects as well as live infants than Male-Cohabited subjects. Additionally, the frequency of self-grooming in Female-Cohabited males was higher for water-covered objects compared to Male-Cohabited males. In presence of water and live infants, Female-Cohabited males groomed themselves with greater frequency than in presence of infant odor or sub-adult odor. The data suggest that female cues increase the male＇s sensitivity to infant odors and enhance the salience of non-social odors.