PubMed · 5527622
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A Robertson. 1970. Some optimum problems in individual selection.. https://doi.org/10.1016/0040-5809(70)90045-6
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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.
Maize silage is a significant energy source for animal production operations, and the efficiency of the conversion of forage into animal mass is an important consideration when selecting cultivars for use as feed. Fiber and lignin are negatively correlated with digestibility of feed, so the development of forage with reduced levels of these cell-wall components (CWCs) is desirable. While variability for fiber and lignin is present in maize germplasm, traditional selection has focused on the yield of the ear rather than the forage quality of the whole plant, and little information is available concerning the genetics of fiber and lignin. The objectives of this study were to map quantitative trait loci (QTLs) for fiber and lignin in the maize stalk and compare them with QTLs from other populations. Stalk samples were harvested from 191 recombinant inbred lines (RILs) of B73 (an inbred line with low-to-intermediate levels of CWCs) x De811 (an inbred line with high levels of CWCs) at two locations in 1998 and one in 1999 and assayed for neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL). The QTLs were detected on nine chromosomes, mostly clustered in concordance with the high genetic correlations between NDF and ADF. Adjustment of NDF for ADF and ADF for ADL revealed that most of the variability for CWCs in this population is in ADF. Many of the QTLs detected in this study have also been detected in other populations, and several are linked to candidate genes for cellulose or starch biosynthesis. The genetic information obtained in this study should be useful to breeding efforts aimed at improving the quality of maize silage.
The value of molecular markers and pedigree records, separately or in combination, to assist in the management of conserved populations has been tested. The general strategy for managing the population was to optimize contributions of parents to the next generation for minimizing the global weighted coancestry. Strategies differed in the type of information used to compute global coancestries, the number and type of evaluated individuals, and the system of mating. Genealogical information proved to be very useful (at least for 10 generations of management) to arrange individuals' contributions via the minimization of global coancestry. In fact, the level of expected heterozygosity after 10 generations yielded by this strategy was 88-100% of the maximum possible improvement obtained if the genotype for all loci was known. Marker information was of very limited value if used alone. The amount and degree of polymorphism of markers to be used to compute molecular coancestry had to be high to mimic the performance of the strategy relying on pedigree, especially in the short term (for example, >10 markers per chromosome with 10 alleles each were needed if only the parents' genotype was available). When both sources of information are combined to calculate the coancestry conditional on markers, clear increases in effective population size (Ne) were found, but observed diversity levels (either gene or allelic diversity) in the early generations were quite similar to the ones obtained with pedigree alone. The advantage of including molecular information is greater when information is available on a greater number of individuals (offspring and parents vs. parents only). However, for realistic situations (i.e., large genomes) the benefits of using information on offspring are small. The same conclusions were reached when comparing the use of the different types of information (genealogical or/and molecular) to perform minimum coancestry matings.