Quantitative trait loci and the study of plant domestication

Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Capsicum annuum L.)

Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F₂:₃ mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.

QTL Analysis of Stem Elongation and Flowering Time in Lettuce Using Genotyping-by-Sequencing

Lettuce plants tend to undergo floral initiation by elongation of flower stalks (bolting) under high-temperature and long-day conditions, which is a serious problem for summer lettuce production. Our objective was to generate a high-density genetic map using SNPs obtained from genotyping-by-sequencing (GBS) analysis of F5 recombinant inbred lines (RILs) and to map QTLs involved in stem growth and flowering time in lettuce. A set of 127 intra-specific RIL mapping populations derived from a cross between two varieties, green and red leaf lettuce, were used to identify QTLs related to the number of days from sowing to bolting (DTB), to flowering of the first flower (DTF), to seed-setting of the first flower (DTS), and the total number of leaves (LN), plant height (PH), and total number of branches of main inflorescence (BN) for two consecutive years. Of the 15 QTLs detected, one that controls DTB, DTF, DTS, LN, and PH detected on LG 7, and another QTL that controls DTF, DTS, and PH detected on LG 1. Analysis of the genomic sequence corresponding to the QTL detected on LG 7 led to the identification of 22 putative candidate genes. A consistent QTL related to bolting and flowering time, and corresponding candidate genes has been reported. This study will be valuable in revealing the genetic basis of stem growth and flowering time in lettuce.

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

Cucurbita maxima Duchesne squash and pumpkins are cultivated world-wide. Cucurbita maxima fruits are produced for fresh market and are valuable for food processing. Therefore, fruit characteristics and yield are the traits of high economic importance for breeders. To date, the genetic basis of fruit-associated traits in C. maxima have been poorly understood. In the present study, we evaluated fruit-associated traits and conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross of two inbred lines with different fruit morphotypes. Phenotypic data for nine fruit traits (earliness, weight, number per plant, yield per plant, length and diameter, shape index, flesh thickness, sucrose content and dry matter content) were collected for RILs in two open-field experiments. Pairwise analysis of the phenotypic data revealed correlations among the fruit and yield-associated traits. Using a previously developed genetic map, we identified 26 QTLs for eight traits. The QTLs were found in 10 locations on eight chromosomes of C. maxima. The QTLs were detected across experiments and explained up to 41.4% of the observed phenotypic variations. Major-effect QTLs for multiple fruit-associated traits were clustered on chromosome 4, suggesting that this genomic region has been under selection during diversification and/or domestication of C. maxima.

Recessive Resistance Governed by a Major Quantitative Trait Locus Restricts Clover Yellow Vein Virus in Mechanically but Not Graft-Inoculated Cultivated Soybeans

Clover yellow vein virus (ClYVV) infects and causes disease in legume plants. However, here, we found that ClYVV isolate No. 30 (ClYVV-No.30) inefficiently multiplied or spread via cell-to-cell movement in mechanically inoculated leaves of a dozen soybean (Glycine max) cultivars and resulted in failure to spread systemically. Soybean plants also had a similar resistance phenotype against additional ClYVV isolates. In contrast, all but one of 24 tested accessions of wild soybeans (G. soja) were susceptible to ClYVV-No.30. Graft inoculation of cultivated soybean TK780 with ClYVV-No.30-infected wild soybean B01167 scion resulted in systemic infection of the cultivated soybean rootstock. This suggests that, upon mechanical inoculation, the cultivated soybean inhibits ClYVV-No.30, at infection steps prior to the systemic spread of the virus, via vascular systems. Systemic infection of all F1 plants from crossing between TK780 and B01167 and of 68 of 76 F2 plants with ClYVV-No.30 indicated recessive inheritance of the resistance. Further genetic analysis using 64 recombinant inbred lines between TK780 and B01167 detected one major quantitative trait locus, designated d-cv, for the resistance that was positioned in the linkage group D1b (chromosome 2). The mapped region on soybean genome suggests that d-cv is not an allele of the known resistance genes against soybean mosaic virus.

Construction of genetic linkage map and genome dissection of domestication-related traits of moth bean (Vigna aconitifolia), a legume crop of arid areas

The moth bean (Vigna aconitifolia), possibly the most primitive crop of the genus Vigna, is a highly drought- and heat-resistant legume grown in arid areas. Moth bean domestication involved phenotypic changes, including reduction of seed dormancy and pod shattering, increased organ size, and earlier flowering and maturity. However, the genetics of the domestication process in moth bean is not known. In this study, we constructed a genetic linkage map for moth bean and used the map to identify quantitative trait loci (QTL) for domestication-related traits of an F₂ population of 188 individuals produced from a cross of wild moth bean (TN67) and cultivated moth bean (ICPMO056). The genetic linkage map comprised 11 linkage groups (LG) of 172 simple sequence repeat markers and spanned a total length of 1016.8 centiMorgan (cM), with an average marker distance of 7.34 cM. A comparative genome analysis showed high genome synteny between moth bean and mungbean (Vigna radiata), adzuki bean (Vigna angularis), rice bean (Vigna umbellata), and yardlong bean (Vigna unguiculata). In total, 50 QTLs and 3 genes associated with 20 domestication-related traits were identified. Most of the QTLs belonged to five LGs (1, 2, 4, 7, and 10). Key traits related to domestication such as seed dormancy and pod shattering were controlled by large-effect QTLs (PVE > 20%) with one or two minor QTLs, whereas all other traits were controlled by one-seven minor QTLs, apart from seed weight, which was controlled by one major and seven minor QTLs. These results suggest that a small number of mutations with large phenotypic effects have contributed to the domestication of the moth bean. Comparative analysis of QTLs with related Vigna crops revealed that there are several domestication-related large-effect QTLs that had not been used in moth bean domestication. This study provides a basic genetic map and identified genome regions associated with domestication-related traits, which will be useful for the genetic improvement of the moth bean and related Vigna species.

Primary Metabolism in Citrus Fruit as Affected by Its Unique Structure

Citrus is one of the world's most important fruit crops, contributing essential nutrients, such as vitamin C and minerals, to the human diet. It is characterized by two important traits: first, its major edible part is composed of juice sacs, a unique structure among fruit, and second, relatively high levels of citric acid are accumulated in the vacuole of the juice sac cell. Although the major routes of primary metabolism are generally the same in citrus fruit and other plant systems, the fruit's unique structural features challenge our understanding of carbon flow into the fruit and its movement through all of its parts. In fact, acid metabolism and accumulation have only been summarized in a few reviews. Here we present a comprehensive view of sugar, acid and amino acid metabolism and their connections within the fruit, all in relation to the fruit's unique structure.

QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis)

QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively. Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F₂ and F_2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber. A linkage map with 267 microsatellite marker loci was developed with 138 F₂ plants. Phenotypic data of male and female flowering time, fruit length and diameter and three other traits (mature fruit weight and number, and seedling hypocotyl length) were collected in multiple environments. Three flowering time QTL, FT1.1, FT5.1 and FT6.2 were identified, in which FT6.2 played the most important role in conferring less photoperiod sensitive early flowering during domestication whereas FT1.1 seemed more influential in regulating flowering time within the cultivated cucumber. Eight consensus fruit size QTL distributed in 7 chromosomes were detected, each of which contributed to both longitudinal and radial growth in cucumber fruit development. Among them, FS5.2 on chromosome 5 exhibited the largest effect on the determination of round fruit shape that was characteristic of the WI7167 XIS cucumber. Possible roles of these flowering time and fruit size QTL in domestication of cucumber and crop evolution of the semi-wild XIS cucumber, as well as the genetic basis of round fruit shape in cucumber are discussed.

Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test

The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.

Selection on crop-derived traits and QTL in sunflower (Helianthus annuus) crop-wild hybrids under water stress

Locally relevant conditions, such as water stress in irrigated agricultural regions, should be considered when assessing the risk of crop allele introgression into wild populations following hybridization. Although research in cultivars has suggested that domestication traits may reduce fecundity under water stress as compared to wild-like phenotypes, this has not been investigated in crop-wild hybrids. In this study, we examine phenotypic selection acting on, as well as the genetic architecture of vegetative, reproductive, and physiological characteristics in an experimental population of sunflower crop-wild hybrids grown under wild-like low water conditions. Crop-derived petiole length and head diameter were favored in low and control water environments. The direction of selection differed between environments for leaf size and leaf pressure potential. Interestingly, the additive effect of the crop-derived allele was in the direction favored by selection for approximately half the QTL detected in the low water environment. Selection favoring crop-derived traits and alleles in the low water environment suggests that a subset of these alleles would be likely to spread into wild populations under water stress. Furthermore, differences in selection between environments support the view that risk assessments should be conducted under multiple locally relevant conditions.

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

BACKGROUND

Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.

RESULTS

A total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified.

CONCLUSIONS

Given the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.

QTL affecting fitness of hybrids between wild and cultivated soybeans in experimental fields

The objective of this study was to identify quantitative trait loci (QTL) affecting fitness of hybrids between wild soybean (Glycine soja) and cultivated soybean (Glycine max). Seed dormancy and seed number, both of which are important for fitness, were evaluated by testing artificial hybrids of G. soja × G. max in a multiple-site field trial. Generally, the fitness of the F₁ hybrids and hybrid derivatives from self-pollination was lower than that of G. soja due to loss of seed dormancy, whereas the fitness of hybrid derivatives with higher proportions of G. soja genetic background was comparable with that of G. soja. These differences were genetically dissected into QTL for each population. Three QTLs for seed dormancy and one QTL for total seed number were detected in the F₂ progenies of two diverse cross combinations. At those four QTLs, the G. max alleles reduced seed number and severely reduced seed survival during the winter, suggesting that major genes acquired during soybean adaptation to cultivation have a selective disadvantage in natural habitats. In progenies with a higher proportion of G. soja genetic background, the genetic effects of the G. max alleles were not expressed as phenotypes because the G. soja alleles were dominant over the G. max alleles. Considering the highly inbreeding nature of these species, most hybrid derivatives would disappear quickly in early self-pollinating generations in natural habitats because of the low fitness of plants carrying G. max alleles.

Rapid evolution in crop-weed hybrids under artificial selection for divergent life histories

When species hybridize, offspring typically exhibit reduced fitness and maladapted phenotypes. This situation has biosafety implications regarding the unintended spread of novel transgenes, and risk assessments of crop-wild hybrids often assume that poorly adapted hybrid progeny will not evolve adaptive phenotypes. We explored the evolutionary potential of early generation hybrids using nontransgenic wild and cultivated radish (Raphanus raphanistrum, Raphanus sativus) as a model system. We imposed four generations of selection for two weedy traits - early flowering or large size - and measured responses in a common garden in Michigan, USA. Under selection for early flowering, hybrids evolved to flower as early as wild lineages, which changed little. These early-flowering hybrids also recovered wild-type pollen fertility, suggesting a genetic correlation that could accelerate the loss of crop traits when a short life cycle is advantageous. Under selection for large size at reproduction, hybrids evolved longer leaves faster than wild lineages, a potentially advantageous phenotype under longer growing seasons. Although early generation hybrid offspring have reduced fitness, our findings provide novel support for rapid adaptation in crop-wild hybrid populations. Biosafety risk assessment programs should consider the possibility of rapid evolution of weedy traits from early generations of seemingly unfit crop-wild hybrids.

A comparative view of the evolution of grasses under domestication

Crop grasses were among the first plants to be domesticated c. 12,000 yr ago, and they still represent the main staple crops for humans. During domestication, as did many other crops, grasses went through dramatic genetic and phenotypic changes. The recent massive increase in genomic data has provided new tools to investigate the genetic basis and consequences of domestication. Beyond the genetics of domestication, many aspects of grass biology, including their phylogeny and developmental biology, are also increasingly well studied, offering a unique opportunity to analyse the domestication process in a comparative way. Taking such a comparative point of view, we review the history of domesticated grasses and how domestication affected their phenotypic and genomic diversity. Considering recent theoretical developments and the accumulation of genetic data, we revisit more specifically the role of mating systems in the domestication process. We close by suggesting future directions for the study of domestication in grasses.

Quantitative genetics in the age of omics

The use of natural variation in the genetic dissection of quantitative traits has a long-standing tradition. Recent advances in high-throughput technologies for the quantification of biological molecules have shifted the focus in quantitative genetics from single traits to comprehensive large-scale analyses. So-called omic technologies now enable geneticists to take a look in the black box that translates genetic information into biological function. These processes include transcriptional and (post) translational regulation as well as metabolic signaling pathways. The progress made in analytical and statistical techniques now allows the construction of regulatory networks that integrate the different levels of the biological information flow from gene-to-function.

Quantitative trait locus analysis of the early domestication of sunflower

Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improved oilseed cultivar, we found that domestication-related traits in sunflower are controlled by numerous QTL, typically of small effect. To provide insight into the minimum genetic changes required to transform the weedy common sunflower into a useful crop plant, we mapped QTL underlying domestication-related traits in a cross between a wild sunflower and a primitive Native American landrace that has not been the target of modern breeding programs. Consistent with the results of the previous study, our data indicate that the domestication of sunflower was driven by selection on a large number of loci, most of which had small to moderate phenotypic effects. Unlike the results of the previous study, however, nearly all of the QTL identified herein had phenotypic effects in the expected direction, with the domesticated allele producing a more crop-like phenotype and the wild allele producing a more wild-like phenotype. Taken together, these results are consistent with the hypothesis that selection during the post-domestication era has resulted in the introduction of apparently maladaptive alleles into the modern sunflower gene pool.

Recursos genéticos y mejoramiento de frutales andinos: una visión conceptual

Los frutales andinos comprenden especies con diversos grados de desarrollo y con potencial importante en los países del área. Su cultivo generalmente se realiza con materiales de agricultor heterogéneos sin aplicación de recomendaciones tecnológicas con enfoque sistémico. La eficiencia productiva y la competitividad de estas especies dependen de la constitución de colecciones de los taxa cultivados y especies relacionadas, debidamente conocidos en sus atributos, que hagan posible el desarrollo de variedades que representen soluciones a problemas limitantes. En el corto plazo la oferta de materiales para la siembra puede basarse en procesos selectivos en las poblaciones locales, con enfoque participativo y clonación de individuos superiores. En el mediano y largo plazos ésta puede enfocarse en la creación de una base genética amplia, enriquecida con atributos de las especies silvestres relacionadas. La selección y clonación masiva deben apoyarse, preferiblemente, en cultivo de tejidos, con propagación de diversos clones para prevenir la vulnerabilidad. Hasta el presente, en Colombia se han conformado colecciones de varios frutales andinos, se han llevado a cabo procesos de caracterización de la variabilidad y se han desarrollado algunas actividades de mejoramiento. Éstas corresponden a domesticación, premejoramiento y mejoramiento en lulo y premejoramiento en tomate de árbol con relación a la incorporación de resistencia a la antracnosis de los frutos. Las experiencias sirven para proponer el desarrollo de una plataforma recursos genéticos/oferta de materiales mejorados, que apoye eficazmente la función productiva desde la óptica genotípica.