A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies

Mating cues evolve rapidly and can contribute to species formation and maintenance. However, little is known about how sexual signals diverge and how this variation integrates with other barrier loci to shape the genomic landscape of reproductive isolation. Here, we elucidate the genetic basis of ultraviolet (UV) iridescence, a courtship signal that differentiates the males of Colias eurytheme butterflies from a sister species, allowing females to avoid costly heterospecific matings. Anthropogenic range expansion of the two incipient species established a large zone of secondary contact across the eastern United States with strong signatures of genomic admixtures spanning all autosomes. In contrast, Z chromosomes are highly differentiated between the two species, supporting a disproportionate role of sex chromosomes in speciation known as the large-X (or large-Z) effect. Within this chromosome-wide reproductive barrier, linkage mapping indicates that cis-regulatory variation of bric a brac (bab) underlies the male UV-iridescence polymorphism between the two species. Bab is expressed in all non-UV scales, and butterflies of either species or sex acquire widespread ectopic iridescence following its CRISPR knockout, demonstrating that Bab functions as a suppressor of UV-scale differentiation that potentiates mating cue divergence. These results highlight how a genetic switch can regulate a premating signal and integrate with other reproductive barriers during intermediate phases of speciation.

Smooth Descent: a Ploidy-Aware Algorithm To Improve Linkage Mapping In The Presence of Genotyping Errors

Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH (van Os et al. 2005), an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. Moreover, the simplicity of the algorithm allows thousands of markers to be efficiently processed, thus being particularly useful for error detection in high-density datasets. We have implemented this algorithm in the R package SmoothDescent.

Evolution of the canonical sex chromosomes of the guppy and its relatives

The sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as humans and Drosophila melanogaster, and they carry many of the genes responsible for the males’ dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here we address these controversies by reviewing the evidence and reanalyzing data. We find no evidence of a nonrecombining sex determining region (SDR) or evolutionary strata in P. reticulata. Further, we find that the data most strongly support the hypothesis that the SDRs of two close relatives of the guppy, P. wingei and Micropoecilia picta, evolved independently after their lineages diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.

BSA‑Seq and Genetic Mapping Reveals AhRt2 as a Candidate Gene Responsible for Red Testa of Peanut

Testa color is an important trait of peanut (Arachis hypogaea L.). Peanuts with red testa are rich in anthocyanin, are very popular with consumers. However, genes responsible for the red testa trait in peanut are rarely reported. In order to fine map red testa gene, two F4 populations were constructed through the cross of YZ9102 (pink testa) with ZH12 (red testa) and Zhanhong2 (red testa). Genetic analysis indicated that red testa was controlled by a single recessive gene, and named as AhRt2 (Red testa gene 2). Using BSA-seq approach, AhRt2 was preliminary identified in chromosome 12, and further mapped to a 530-kb interval using 220 recombinant lines through linkage mapping. Functional annotation, expression profiling, and sequence variation analyses confirmed that the anthocyanin reductase (ANR), Arahy.IK60LM, was the most likely candidate gene for AhRt2. A SNP in the third exon of AhRt2 changed the encoding amino acids, was associated with red testa of peanut. In addition, a closely linkaged molecular marker to red testa trait was developed. Our result provide insight into the molecular mechanism underlying peanut testa color and provide valuable diagnostic marker for marker-assisted selected (MAS) breeding in peanut.

Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte

Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. Results In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. Conclusion Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.

Discovery and Validation of a Recessively Inherited Major-Effect QTL Conferring Resistance to Maize Lethal Necrosis (MLN) Disease

Maize lethal necrosis (MLN) is a viral disease with a devastating effect on maize production. Developing and deploying improved varieties with resistance to the disease is important to effectively control MLN; however, little is known about the causal genes and molecular mechanism(s) underlying MLN resistance. Screening thousands of maize inbred lines revealed KS23-5 and KS23-6 as two of the most promising donors of MLN resistance alleles. KS23-5 and KS23-6 lines were earlier developed at the University of Hawaii, United States, on the basis of a source population constituted using germplasm from Kasetsart University, Thailand. Both linkage mapping and association mapping approaches were used to discover and validate genomic regions associated with MLN resistance. Selective genotyping of resistant and susceptible individuals within large F2 populations coupled with genome-wide association study identified a major-effect QTL (qMLN06_157) on chromosome 6 for MLN disease severity score and area under the disease progress curve values in all three F2 populations involving one of the KS23 lines as a parent. The major-effect QTL (qMLN06_157) is recessively inherited and explained 55%–70% of the phenotypic variation with an approximately 6 Mb confidence interval. Linkage mapping in three F3 populations and three F2 populations involving KS23-5 or KS23-6 as one of the parents confirmed the presence of this major-effect QTL on chromosome 6, demonstrating the efficacy of the KS23 allele at qMLN06.157 in varying populations. This QTL could not be identified in population that was not derived using KS23 lines. Validation of this QTL in six F2 populations with 20 SNPs closely linked with qMLN06.157 was further confirmed its consistent expression across populations and its recessive nature of inheritance. On the basis of the consistent and effective resistance afforded by the KS23 allele at qMLN06.157, the QTL can be used in both marker-assisted forward breeding and marker-assisted backcrossing schemes to improve MLN resistance of breeding populations and key lines for eastern Africa.

Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq

Salinity is a major abiotic stress that limits plant growth and crop productivity. Indica rice and japonica rice show significant differences in tolerance to abiotic stress, and it is considered a feasible method to breed progeny with stronger tolerance to abiotic stress by crossing indica and japonica rice. We herein developed a high-generation recombinant inbred lines (RILs) from Luohui 9 (indica) X RPY geng (japonica). Based on the high-density bin map of this RILs population, salt tolerance QTLs controlling final survival rates were analyzed by linkage mapping and RTM-GWAS methods. A total of seven QTLs were identified on chromosome 3, 4, 5, 6, and 8. qST-3.1, qST-5.1, qST-6.1, and qST-6.2 were novel salt tolerance QTLs in this study and their function were functionally verified by comparative analysis of parental genotype RILs. The gene aggregation result of these four new QTLs emphasized that the combination of the four QTL synergistic genotypes can significantly improve the salt stress tolerance of rice. By comparing the transcriptomes of the root tissues of the parents’ seedlings, at 3 days and 7 days after salt treatment, we then achieved fine mapping of QTLs based on differentially expressed genes (DEGs) identification and DEGs annotations, namely, LOC_Os06g01250 in qST-6.1, LOC_Os06g37300 in qST-6.2, LOC_Os05g14880 in qST-5.1. The homologous genes of these candidate genes were involved in abiotic stress tolerance in different plants. These results indicated that LOC_Os05g14880, LOC_Os06g01250, and LOC_Os06g37300 were the candidate genes of qST-5.1, qST-6.1, and qST-6.2. Our finding provided novel salt tolerance-related QTLs, candidate genes, and several RILs with better tolerance, which will facilitate breeding for improved salt tolerance of rice varieties and promote the exploration tolerance mechanisms of rice salt stress.

Linkage and QTL mapping for tuber shape and specific gravity in a tetraploid mapping population of potato representing the russet market class

Background Tuber shape and specific gravity (dry matter) are important agronomic traits in potato processing and impact production costs, quality, and consistency of the final processed food products such as French fries and potato chips. In this study, linkage and QTL mapping were performed for these two traits to allow for the implementation of marker-assisted selection to facilitate breeding efforts in the russet market class. Two parents, Rio Grande Russet (female) and Premier Russet (male) and their 205 F1 progenies were initially phenotyped for tuber shape and specific gravity in field trials conducted in Idaho and North Carolina in 2010 and 2011, with specific gravity also being measured in Minnesota in 2011. Progenies and parents were previously genotyped using the Illumina SolCAP Infinium 8303 Potato SNP array, with ClusterCall and MAPpoly (R-packages) subsequently used for autotetraploid SNP calling and linkage mapping in this study. The 12 complete linkage groups and phenotypic data were then imported into QTLpoly, an R-package designed for polyploid QTL analyses. Results Significant QTL for tuber shape were detected on chromosomes 4, 7, and 10, with heritability estimates ranging from 0.09 to 0.36. Significant tuber shape QTL on chromosomes 4 and 7 were specific to Idaho and North Carolina environments, respectively, whereas the QTL on chromosome 10 was significant regardless of growing environment. Single marker analyses identified alleles in the parents associated with QTL on chromosomes 4, 7, and 10 that contributed to significant differences in tuber shape among progenies. Significant QTL were also identified for specific gravity on chromosomes 1 and 5 with heritability ranging from 0.12 to 0.21 and were reflected across environments. Conclusion Fully automated linkage mapping and QTL analysis were conducted to identify significant QTL for tuber shape and dry matter in a tetraploid mapping population representing the russet market class. The findings are important for the development of molecular markers useful to potato breeders for marker-assisted selection for the long tuber shape and acceptable dry matter required by the potato industry within this important market class.