Polymorphisms for genetic and ecological systems with weak coupling.

Cis-regulatory elements (CREs) are the genetic DNA fragments bound by transcription factors (TFs). CREs function as molecular switches that precisely modulate the dosage and spatiotemporal patterns of gene expression. The systematic identification of CREs not only facilitates the annotation of the functional non-coding genome but also provides essential insights into the architecture of gene regulatory networks and sheds light on an accurate selection of the target sites for genetic engineering of crops. In this review, we summarize the current high-throughput methodologies used for identifying CREs, illustrate the associations between CREs and agronomic traits in horticultural crops, and discuss how CREs can be exploited to facilitate crop breeding.

Breeding↗

PubMed2007

Patch aging and the S-Allee effect: breeding system effects on the demographic response of plants to habitat fragmentation.

We used empirical and modeling approaches to examine effects of plant breeding systems on demographic responses to habitat fragmentation. Empirically, we investigated effects of local flowering plant density on pollination and of population size on mate availability in a common, self-incompatible purple coneflower, Echinacea angustifolia, growing in fragmented prairie habitat. Pollination and recruitment increased with weighted local density around individual flowering plants. This positive density dependence is an Allee effect. In addition, mean mate compatibility between pairs of plants increased with population size. Based on this empirical study, we developed an individual-based, spatially explicit demographic model that incorporates autosomal loci and an S locus. We simulated habitat fragmentation in populations identical except for their breeding system, self-incompatible (SI) or self-compatible (SC). Both populations suffered reduced reproduction in small patches because of scarcity of plants within pollination distance (potential mates) and inbreeding depression. But SI species experienced an additional, genetic contribution to the Allee effect (S-Allee effect) caused by allele loss at the S locus, which reduces mate availability, thereby decreasing reproduction. The strength of the S-Allee effect increases through time (i.e., patches age) because random genetic drift reduces S-allele richness. We investigate how patch aging influences extinction and discuss how the S-Allee effect influences communities in fragmented habitat.

Breeding↗

PubMed2007

Capturing diversity in the cereals: many options but little promiscuity.

It is generally recognized by geneticists and plant breeders alike that there is a need to further improve the ability to capture and manipulate genetic diversity. The effective harnessing of diversity in traditional breeding programmes is limited and, therefore, it is vital that meiotic recombination can be manipulated given that it plays a pivotal role in generating diversity. With the advent of a wider range of genomics technologies, our understanding of meiotic processes should increase rapidly. Although comparative genetics has been useful, particularly in the broader grass family, the development of physical maps, long-range sequencing and transcript profiles promises to unravel the complexities of genomes as large or larger than wheat. Highlighting the most significant findings to date, this review pools the knowledge on these tools and reproductive processes.

Breeding↗