indirect selection
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Author(s):  
Brian Charlesworth ◽  
Jeffrey Jensen

We write to address recent claims by Gompert et al. (2021) about the potentially important and underappreciated phenomena of “indirect selection”, the observation that neutral regions may be affected by natural selection. We argue both that this phenomenon – generally known as genetic hitchhiking – is neither new nor poorly studied, and that the patterns described by the authors have multiple alternative explanations.


2021 ◽  
Author(s):  
Yevgeniy Raynes ◽  
Daniel M Weinreich

Ploidy - the number of homologous chromosome sets in a cell - is remarkably variable across the natural world, yet the evolutionary processes that have resulted in such diversity remain poorly understood. Here we use stochastic agent-based simulations to model ploidy evolution under the influence of indirect selection, i.e., selection mediated solely by statistical associations with fitness-affecting mutations. We find that in non-equilibrium asexual populations, the sign of selection on ploidy can change with population size - a phenomenon we have previously termed sign inversion. In large populations, ploidy dynamics are dominated by indirect effects of selection on beneficial mutations, which favors haploids over diploids. However, as population size declines, selection for beneficial mutations is neutralized by random genetic drift before drift can overwhelm selection against the cost of the deleterious mutational load. As a result, in small populations indirect selection is dominated by the cost of the deleterious load, which favors diploids over haploids. Our work adds to the growing body of evidence challenging established evolutionary theory that population size can affect only the efficiency, but not the sign, of natural selection.


2021 ◽  
Vol 12 ◽  
Author(s):  
Paolo Annicchiarico ◽  
Nelson Nazzicari ◽  
Tommaso Notario ◽  
Cristina Monterrubio Martin ◽  
Massimo Romani ◽  
...  

Mixed stand (MS) cropping of pea with small-grain cereals can produce more productive and environment-friendly grain crops relative to pure stand (PS) crops but may require selection to alleviate the pea competitive disadvantage. This study aimed to assess the pea variation for competitive ability and its associated traits and the efficiency of four phenotypic or genomic selection strategies. A set of 138 semi-leafless, semi-dwarf pea lines belonging to six recombinant inbred line populations and six parent lines were genotyped using genotyping-by-sequencing and grown in PS and in MS simultaneously with one barley and one bread wheat cultivar in two autumn-sown trials in Northern Italy. Cereal companions were selected in a preliminary study that highlighted the paucity of cultivars with sufficient earliness for association. Pea was severely outcompeted in both years albeit with variation for pea proportion ranging from nearly complete suppression (<3%) to values approaching a balanced mixture. Greater pea proportion in MS was associated with greater total yield of the mixture (r ≥ 0.46). The genetic correlation for pea yield across MS and PS conditions slightly exceeded 0.40 in both years. Later onset of flowering and taller plant height at flowering onset displayed a definite correlation with pea yield in MS (r ≥ 0.46) but not in PS, whereas tolerance to ascochyta blight exhibited the opposite pattern. Comparisons of phenotypic selection strategies within or across populations based on predicted or actual yield gains for independent years indicated an efficiency of 52–64% for indirect selection based on pea yield in PS relative to pea yield selection in MS. The efficiency of an indirect selection index including onset of flowering, plant height, and grain yield in PS was comparable to that of pea yield selection in MS. A genome-wide association study based on 5,909 SNP markers revealed the substantial diversity of genomic areas associated with pea yield in MS and PS. Genomic selection for pea yield in MS displayed an efficiency close to that of phenotypic selection for pea yield in MS, and nearly two-fold greater efficiency when also taking into account its shorter selection cycle and smaller evaluation cost.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Laxman Adhikari ◽  
Shiva O. Makaju ◽  
Orville M. Lindstrom ◽  
Ali M. Missaoui

Abstract Background Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were tested for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping-by-sequencing (GBS) and the quantitative trait loci (QTL) associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. Results Alfalfa FT screening method optimized in this experiment comprises three major steps: clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is a useful indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL associated with four traits; nine for visual rating-based FT, five for percentage survival (PS), four for treated to control regrowth ratio (RR), and two for treated to control biomass ratio (BR). Some QTL positions overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) were from the potential genic region for a cold tolerance gene CBF. The BLAST alignment of a CBF sequence of M. truncatula, a close relative of alfalfa, against the alfalfa reference showed that the gene’s ortholog resides around 75 Mb on chromosome 6. Conclusions The indoor freezing tolerance selection method reported is useful for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources for the research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.


Author(s):  
Diógenes Cecchin Silveira ◽  
Simone Meredith Scheffer Basso ◽  
Luciano Antônio Ebone ◽  
Andréia Caverzan ◽  
Juliana Medianeira Machado ◽  
...  

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1510
Author(s):  
Samuel Henrique Kamphorst ◽  
Gabriel Moreno Bernardo Gonçalves ◽  
Antônio Teixeira do Amaral Júnior ◽  
Valter Jário de Lima ◽  
Kátia Fabiane Medeiros Schmitt ◽  
...  

The identification of traits associated with drought tolerance in popcorn is a contribution to support selection of superior plants under soil water deficit. The objective of this study was to choose morphological traits and the leaf greenness index, measured on different dates, to estimate grain yield (GY) and popping expansion (PE), evaluated in a set of 20 popcorn lines with different genealogies, estimated by multiple regression models. The variables were divided into three groups: morpho-agronomic traits—100-grain weight (GW), prolificacy (PR), tassel length (TL), number of tassel branches, anthesis-silking interval, leaf angle (FA) and leaf rolling (FB); variables related to the intensity of leaf greenness during the grain-filling period, at the leaf level, measured by a portable chlorophyll meter (SPAD) and at the canopy level, calculated as the normalized difference vegetation index (NDVI). The inbred lines were cultivated under two water conditions: well-watered (WW), maintained at field capacity, and water stress (WS), for which irrigation was stopped before male flowering. The traits GY (55%) and PE (28%) were most affected by water restriction. Among the morpho-agronomic traits, GW and PR were markedly reduced (>10%). Under dry conditions, the FA in relation to the plant stalk tended to be wider, the FB curvature greater and leaf senescence accelerated (>15% at 22 days after male flowering). The use of multiple regression for the selection of predictive traits proved to be a useful tool for the identification of groups of adequate traits to efficiently predict the economically most important features of popcorn (GY and PE). The SPAD index measured 17 days after male flowering proved useful to select indirectly for GY, while, among the morphological traits, TL stood out for the same purpose. Of all traits, PR was most strongly related with PE under WS, indicating its use in breeding programs. The exploitation of these traits by indirect selection is expected to induce increments in GY and PE.


Rice Science ◽  
2021 ◽  
Vol 28 (4) ◽  
pp. 368-378
Author(s):  
Muhammad Fuad Anshori ◽  
Bambang Sapta Purwoko ◽  
Iswari Saraswati Dewi ◽  
Sintho Wahyuning Ardie ◽  
Willy Bayuardi Suwarno

Author(s):  
Shreya Singh ◽  
Rajesh Kanwar ◽  
R.K. Kapila ◽  
K.C. Dhiman

Background: Soybean is an important oilseed crop but it has poor seed longevity. Studies on seed longevity are very complex and hence, an indirect selection criterion should be identified. In this study, seed longevity and its association with agronomic traits of seven soybean varieties was evaluated in the year 2019-2020.Methods: Seed were kept for storage under ambient conditions for a period of 16 months (January 2019 to May 2020). Their germination was recorded at bimonthly intervals and seed longevity was inferred as the time period in months up to which the seed maintains its germination percentage above IMSCS.Result: Accordingly, Palam Early Soya 1 and Him Palam Hara Soya were classified as having short seed longevity (12 months). Hara Soya, Shivalik, Him Soya and Palam Soya were classified as having medium seed longevity (14 months). Whereas, PS 1556 was classified as having long seed longevity ( greater than 16 months). Further, it was found that seed longevity was positively associated with number of pods per plant and seed yield, and negatively associated with number of branches per plant and 100-seed weight. This study presents an indirect selection criterion based on some easily accessible parameters which have strong association with seed longevity.


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