Population genetics and genome‐wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce

Abstract

Genetic diversity is an important resource in crop breeding to improve cultivars with desirable traits. Selective breeding can lead to a reduction of genetic diversity. However, our understanding on this subject remains limited in lettuce (Lactuca sativa L.). Genotyping-by-sequencing (GBS) can provide a reduced version of the genome as a cost-effective method to identify genetic variants across the genome. We genotyped a diverse set of 441 lettuce accessions using the GBS method. Phylogenetic and population genetic analyses indicated substantial genetic divergence among four horticultural types of lettuce: butterhead, crisphead, leaf, and romaine. Genetic-diversity estimates between and within the four types indicated that the crisphead type was the most differentiated from other types, whereas its population was the most homogenous with the slowest linkage disequilibrium (LD) decay among the four types. These results suggested that crisphead lettuces had relatively less genetic variation across the genome as well as low gene flow from other types. We identified putative selective sweep regions that showed low genetic variation in the crisphead type. Genomewide association study (GWAS) and quantitative trait loci (QTL) analyses provided evidence that these genomic regions were, in part, associated with delayed bolting, implicating the positive selection of delayed bolting in reducing variation. Our findings enhance the current understanding of genetic diversity and the impacts of selective breeding on patterning genetic variation in lettuce.

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

“…Therefore, our sequence data could be used in subsequent analysis. Moreover, we obtained a transition/transversion ratio of 3.51, which was higher than those obtained for common bean (1.27) [ 44 ], apricot (1.78–1.79) [ 51 ], and lettuce (2.10) [ 52 ], but lower than that previously reported for tea (4.02) [ 15 ]. Thus, transitions better tolerated the natural resistance and might have consisted of synonymous mutations in protein-coding sequences [ 53 ].…”

Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

“…Our results showed that another feature of Baekdadagi-specific genetically diverse genomic regions is maintenance of genetic diversity; however, this diversity was not distributed evenly across the cucumber genomes. These results are consistent with selective sweep events which happened during domestication and modern breeding in mung bean and lettuce [38,39]. Putative selective sweep regions of both crops were also not distributed evenly.…”

Population Structure Analysis Revealed Water or Ancient Hub-induced Genetic Diversity of Cultivated-type Tea Plants in Guizhou Plateau

“…We generated 255.2 Gb clean data from 253 tea accessions with an average of 1.00 Gb clean data per accession, and identi ed 112,072 high-quality SNPs, which was higher than the data reported in the previous study. Moreover, the transition/transversion rate was 3.51, which was higher than those in common bean (Phaseolus vulgaris L.) (1.27) [37], apricot (1.78~1.79) [39] and lettuce (2.10) [40] and lower than the previous report of tea plant (4.02) [14]. This result suggested that transitions were better tolerated the natural resistance, which could be that they were synonymous mutations in protein-coding sequences [41].…”