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However, modern breeding programs have focused on developing high-yield crops by primarily selecting the above-ground phenotype and applying full fertilization during breeding processes, which probably selects against root traits that are important for nutrient uptake efficiency.
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The special expression patterns of these genes may be related to key traits under strong selection during domestication and/or breeding processes (see below), which might be due to regulatory changes.
Perhaps strong allelic variation for plastochron/phyllochron genes is not compatible with extreme earliness and satisfactory crop production, in such a way that strong plastochron/phyllochron new early alleles were (are) eliminated unconsciously during the domestication and/or the breeding processes.
This information can be used to predict particular haplotypes associated with desirable phenotypes during the Japanese rice breeding process, and help in using such haplotype blocks for rice improvement.
Selection of favorable alleles during the domestication and breeding process lead to the generation of new varieties adapted to different climate conditions.
The farmers, during the sampling period, did not have cattle, poultry or other livestock animals in breeding process at their premises.
This implied that selection biases had occurred in partial regions of the genomes during the breeding processes.
Nevertheless, breeding for agronomic traits often occurs in detriment of the organoleptic quality of the fruit, as was demonstrated in the cases of "greek basil", strawberry, and tomato, where most of the typical aromas were lost during recent breeding processes [ 1- 3].
Most of these genotypes have xa5 and Xa4 which were introduced during the breeding process of these varieties.
High resolution graphical genotype indicated genome-level similarities and common genetic events during the breeding process: five xyloglucan fucosyltransferase from O. glaberrima were introgressed in common.
This deviation from the expectation that about one-fourth of the Tongil genome originated from the japonica parent is likely due to the results of selection during the breeding process and/or to segregation distortion in favor of the indica genome because indica-type alleles and plants are favored among hybrid progenies from indica/japonica crosses (Harushima et al. [1996]; Lin et al. [1992]).
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