Common carp are among the oldest domesticated fish in the world. As such, there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection. Hebao red carp (HB, Cyprinus carpio wuyuanensis), an indigenous strain in China, is renowned for its unique body morphology and reddish skin. To reveal the genetic basis underlying the distinct skin color of HB, we constructed an improved high-fidelity (HiFi) HB genome with good contiguity, completeness, and correctness. Genome structure comparison was conducted between HB and a representative wild strain, Yellow River carp (YR, C. carpio haematopterus), to identify structural variants and genes under positive selection. Signatures of artificial selection during domestication were identified in HB and YR populations, while phenotype mapping was performed in a segregating population generated by HB×YR crosses. Body color in HB was associated with regions with fixed mutations. The simultaneous mutation and superposition of a pair of homologous genes ( mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB. Transcriptome analysis of common carp with different alleles of the mitfa mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids. This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp.
鲤鱼是世界上人工养殖最早的鱼类之一。由于长期的自然选择和人工选择，形成了多种食用和观赏用的鲤鱼品系，具有丰富的表型差异。荷包红鲤是中国本土的一个鲤鱼品种，因其独特的外型和红色皮肤而得名。为了揭示荷包红鲤独特体色背后的遗传学机制，我们组装了荷包红鲤新版本HiFi基因组，该基因组具有良好的连续性、完整性和准确性。通过对荷包红鲤与黄河鲤的基因组结构比较，鉴定基因组中的结构变异和受到正选择的基因。荷包红鲤与黄河鲤的群体遗传学分析，鉴定到基因组上的人工选择信号。对荷包红鲤与黄河鲤的杂交子代进行体色性状的GWAS定位，发现鉴定到的候选区段与选择信号重合。A06和B06号染色体上 mitfa基因的两个拷贝同时突变并叠加，导致了荷包红鲤的红色体色。选取具有不同突变类型的杂交子代进行皮肤转录组分析，进一步证实了异源四倍体中基因的加倍能够缓冲基因突变带来的有害效应。该研究为异源四倍体物种的表型-基因型关联提供了新见解，为鲤鱼未来的选育奠定基础。.

Wild plant species provide excellent examples of qualitative traits that evolve in response to environmental challenges (e.g., flower color, heavy metal tolerance, cyanogenesis, and male sterility). In addition to such discrete characters, a dazzling array of continuously distributed, quantitative traits are expressed at every phase of the life cycle. These traits are known or suspected to have evolved by natural selection because they are heritable, differ among populations or closely related taxa occupying distinct habitats, and have individual phenotypes associated with survival and reproductive success. This special issue [American Journal of Botany 109(11)] focuses on the tools and approaches for detecting or inferring the ecological and genetic factors contributing to changes in genetically based variation of quantitative traits within or among populations, or causing their divergence among taxa. The assembled articles use one or more of three primary approaches to detect the process or outcome of natural selection on morphological, life history, reproductive, chemical, and physiological quantitative traits: the analysis of phenotypic or artificially imposed selection to detect direct and indirect selection on traits whose function is well-understood; common garden experiments, including reciprocal transplants and \"resurrection\" experiments; and quantitative genetic analyses designed to detect and to estimate the environmental and genetic sources of phenotypic variation or to forecast short-term evolutionary change. Together, these articles examine and reveal the adaptive capacity of quantitative traits and the genetically based constraints that may limit their directional evolutionary change, thereby informing and testing inferences, hypotheses, and predictions concerning the evolutionary trajectories of wild plant species.

Rapid detection of allelic variation and identification of advantage haplotypes responsible for spike related traits play a crucial role in wheat yield improvement. The released genome sequence of hexaploid wheat (Chinese Spring) provides an extraordinary opportunity for rapid detection of natural variation and promotes breeding application. Here, selection signals detection and genome-wide association study (GWAS) were conducted for spike related traits. Based on the genotyping results by 90K SNP chip, 192 common wheat samples from southwest China were analyzed. One hundred and forty-six selective windows and one hundred and eighty-four significant SNPs (51 for spike length, 28 for kernels per spike, 39 for spikelet number, 30 for thousand kernel weight, and 36 for spike number per plant) were detected. Furthermore, tightly linkage and environmental stability window clusters and SNP clusters were also obtained. As a result, four SNP clusters associated with spike length were detected on chromosome 2A, 2B, 2D, and 6A. Two SNP clusters correlated to kernels per spike were detected on 2A and 2B. One pleiotropy SNP cluster correlated to spikelet number and kernels per spike was detected on 7B. According to the genome sequence, these SNP clusters and their overlapped/flanking QTLs which have been reported previously were integrated to a physical map. The candidate genes responsible for spike length, kernels per spike and spikelet number were predicted. Based on the genotypes of cultivars in south China, two advantage haplotypes associated with spike length and one advantage haplotype associated with kernels per spike/spikelet number were detected which have not been effectively transited into cultivars. According to these haplotypes, KASP markers were developed and diagnosed across landraces and cultivars which were selected from south and north China. Consequently, KASP assay, consistent with the GWAS results, provides reliable haplotypes for MAS in wheat yield improvement.

Pearl oyster Pinctada fucata is widely cultured to produce seawater pearl in South China, and the quality of pearl is significantly affected by its shell color. Thus the Pearl Oyster Selective Breeding Program (POSBP) was carried out for the shell color and growth traits. The black (B), gold (G), red (R) and white (W) shell strains with fast growth trait were achieved after five successive generation selection. In this study, AFLP technique was used to scan genome of four strains with different shell colors to identify the candidate markers under artificial selection. Eight AFLP primer combinations were screened and yielded 688 loci, 676 (98.26%) of which were polymorphic. In black, gold, red and white strains, the percentage of polymorphic loci was 90.41%, 87.79%, 93.60% and 93.31%, respectively, Nei\'s gene diversity was 0.3225, 0.2829, 0.3221 and 0.3292, Shannon\'s information index was 0.4801, 0.4271, 0.4825 and 0.4923, and the value of FST was 0.1805. These results suggested that the four different shell color strains had high genetic diversity and great genetic differentiation among strains, which had been subjected to the continuous selective pressures during the artificial selective breeding. Furthermore, six outlier loci were considered as the candidate markers under artificial selection for shell color. This study provides a molecular evidence for the inheritance of shell color of P. fucata.