A statistical design for testing apomictic diversification through linkage analysis

Abstract

The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic differences at various levels from genotypes to species. The design is based on two reciprocal crosses between two individuals each chosen from a hermaphrodite or monoecious species. A multinomial distribution likelihood is constructed by combining marker information from two crosses. The EM algorithm is implemented to estimate the rate of apomixis and test its difference between two plant populations or species as the parents. The design is validated by computer simulation. A real data analysis of two reciprocal crosses between hickory (Carya cathayensis) and pecan (C. illinoensis) demonstrates the utilization and usefulness of the design in practice. The design provides a tool to address fundamental and applied questions related to the evolution and breeding of apomixis.

Development of SSR Markers in Hickory (Carya cathayensis Sarg.) and Their Transferability to Other Species of Carya

“…Similar results are obtained and described in this paper, which is that the SSR markers developed from hickory are transferable to C. dabieshanensis , C. hunanensis and pecan . Apomixis is also found in pecan [23] and a transferability rate of 63.02% is observed between hickory and pecan here. In addition, it seems that types of mechanism responsible for apomixis in hickory and pecan are different for the fact that there is monomorphism in hickory tested by SSR markers but polymorphism among accessions of pecan, the latter of which is similar to the case in Kentucky bluegrass [18].…”

“…Since pecan has been used in the reciprocal cross with hickory to study apomixis [14, 23], sequencing of PCR fragments of pecan DNAs amplified with all the SSR primers developed from hickory was conducted. As a result, 276 pairs of primers were amplifiable but finally 196 pairs of primers were confirmed to have SSRs contained in their PCR products (Appendix 1), out of which 121 pairs could be used to distinguish hickory from pecan.…”

“…It has been embryologically confirmed that hickory is an apomictic species with a certain rate of outcross [13, 23]. Apomixis was reported to be regulated by a single master regulatory gene or by a gene complex comprising of several tightly linked genes that were located in a recombinationally suppressed region [15-17], which was observed in Oryza sativa [15, 27], Paspalum simplex [28], Tripsacum dactyloides [29], et al When compared with their sexual relatives, apomictic species had cosegregated fragments that had a length of 15 – 40 cM [15], which could be regarded as a singly inherited Mendelian trait [30].…”

A unified DNA sequence and non‐DNA sequence mapping model of complex traits

“…For those outcrossing species that undergo both outcrossing and selfing pollination, we can formulate a mixture model that distinguishes the same genotype formed by selfing and outcrossing, for which the EM algorithm is implemented to estimate outcrossing rate (Li et al ., ). In addition, some plants are apomictic, for which a mixture model can be similarly specified to estimate the proportion of progeny with the same genotype derived from apomictic and meiotic processes (Hou et al ., ; Yin et al ., ; Zeng et al ., 2014b). Outcrossing rate and apomictic fraction are two important parameters that can characterize population structure, diversity and evolution.…”

A unifying experimental design for dissecting tree genomes

“…First, by constructing the linkage-LD map, it can be embraced as a tool for inferring the origin and evolutionary process of natural populations. Second, this design, when implemented with an efficient algorithm, allows estimates of many additional population genetic parameters, such as outcrossing rate [29], apomixis rate [30][31][32], and genetic interference [33], thereby enhancing population and evolutionary genetic Á across genetic distance in cM for canine multigenerational pedigrees [9]. D 0 ab values were estimated from a traditional sampling strategy for LD analysis by Weir's [21] collapsed approach, whereas the recombination rates estimated from meiotic information occurring in artificial crosses.…”