Evolutionary insights into plant breeding

Turner, Sarah D.; Mabry, Makenzie E.; Beissinger, Timothy; Ross‐Ibarra, Jeffrey; Pires, J. Chris

doi:10.1016/j.pbi.2020.03.003

Cited by 40 publications

(18 citation statements)

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“…In general, selective breeding (i.e., artificial selection) causes a new beneficial allele to be fixed rapidly with increased frequency in the population, which can lead to the reduction or elimination of genetic variation over the desired allele and nearby regions. Such rapid fixation of beneficial alleles is called a selective sweep (Turner‐Hissong, Mabry, Beissinger, Ross‐Ibarra, & Pires, 2020; Yamasaki, Wright, & McMullen, 2007). Given the lowest genetic diversity as well as the highest LD decay in the crisphead type, we questioned whether artificial selection influenced its patterns of genetic variation.…”

Section: Resultsmentioning

confidence: 99%

“…Selective sweeps are believed to result from strong positive selection for beneficial traits (Turner‐Hissong et al., 2020). Given its importance in lettuce yield, delayed bolting would be one such candidate trait.…”

Section: Resultsmentioning

confidence: 99%

“…However, the effect is likely limited to the regions associated with desired alleles, and the positive selection alone might be insufficient to explain the reduced genetic variation across the genome. In general, crop breeding occurs on a relatively short time scale, thus predominantly relying on existing genetic diversity, and the practice of artificial selection on a limited gene pool can lead to population bottlenecks (i.e., founder effects), which consequently lead to reduced genetic variation (Hyten et al., 2006; Turner‐Hissong et al., 2020). Reduced genetic diversity in the crisphead type may be attributed to this population bottleneck effect.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…In general, when individuals with distant relationships cross, the offspring may have high genetic diversity. Conversely, if the individual is a closely related cross, then the genetic is low (Acquaah 2017;Turner-Hissong et al 2020).…”

Section: Discussionmentioning

confidence: 99%

Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers

Mursyidin

Khairullah

2020

Biodiversitas

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Abstract. Mursyidin DH, Khairullah I. 2020. Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers. Biodiversitas 21: 4795-4803. A total of 71 cultivars of the tidal swamp rice (Oryza sativa L.), originated mainly from South Kalimantan, Indonesia, were evaluated agro-morphologically by using 26 qualitative and 13 quantitative traits. Based on these traits, this germplasm is generally low in diversity. However, three agro-morphological traits, namely the tillering abilities, seedling height, and diameter of the basal internode, shows the relatively highest diversity, shown by the Lakatan Putih, Pandak Putih, and Bayar Papuyu, respectively. The UPGMA and PCA revealed that this germplasm divided into six main clusters, where the sixth cluster is the largest with a total membership of 60 cultivars. The cluster analysis also revealed that Lakatan Siam is far separate from other cultivars. Thus, this finding might be useful in the future rice breeding programs, particularly in developing new rice cultivar for the tidal swamp areas.

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“…Crop wild relatives (CWRs) provide pools of allelic diversity that at one time were shared through a common ancestor with cultivated relatives. Although Vavilov recognized the potential of CWRs in the early 1900s ( Vavilov 1926 ), advances in genomics and genome editing techniques have enabled scientists to better realize the potential of CWRs as a source of diversity and novel traits for the improvement of cultivated populations ( Prohens et al 2017 ; Li et al 2018 ; Fernie and Yan 2019 ; Khoury et al 2020 ; Turner-Hissong et al 2020 ). Yet these scientific advancements are hindered in that we still have not identified the CWRs of many important crop species.…”

Section: Introductionmentioning

confidence: 99%

The Evolutionary History of Wild, Domesticated, and FeralBrassica oleracea(Brassicaceae)

Mabry

Turner

Gallagher

et al. 2021

Molecular Biology and Evolution

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Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.

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Evolutionary insights into plant breeding

Cited by 40 publications

References 83 publications

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

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

Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers

The Evolutionary History of Wild, Domesticated, and FeralBrassica oleracea(Brassicaceae)

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