Mapping of QTL associated with rice cooking quality and candidate gene analysis / 生物工程学报

Excavating the quantitative trait locus (QTL) associated with rice cooking quality, analyzing candidate genes, and improving cooking quality-associated traits of rice varieties by genetic breeding can effectively improve the taste of rice. In this study, we used the indica rice HZ, the japonica rice Nekken2 and 120 recombinant inbred lines (RILs) populations constructed from them as experimental materials to measure the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) of rice at the maturity stage. We combined the high-density genetic map for QTL mapping. A total of 26 QTLs associated with rice cooking quality (1 QTL associated with GT, 13 QTLs associated with GC, and 12 QTLs associated with AC) were detected, among which the highest likelihood of odd (LOD) value reached 30.24. The expression levels of candidate genes in the localization interval were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and it was found that the expression levels of six genes were significantly different from that in parents. It was speculated that the high expression of LOC_Os04g20270 and LOC_Os11g40100 may greatly increase the GC of rice, while the high expression of LOC_Os01g04920 and LOC_Os02g17500 and the low expression of LOC_Os03g02650 and LOC_Os05g25840 may reduce the AC. The results lay a molecular foundation for the cultivation of new high-quality rice varieties, and provide important genetic resources for revealing the molecular regulation mechanism of rice cooking quality.

Breeding for low cadmium accumulation cereals / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Cadmium (Cd) is an element that is nonessential and extremely toxic to both plants and human beings. Soil contaminated with Cd has adverse impacts on crop yields and threatens human health via the food chain. Cultivation of low-Cd cultivars has been of particular interest and is one of the most cost-effective and promising approaches to minimize human dietary intake of Cd. Low-Cd crop cultivars should meet particular criteria, including acceptable yield and quality, and their edible parts should have Cd concentrations below maximum permissible concentrations for safe consumption, even when grown in Cd-contaminated soil. Several low-Cd cereal cultivars and genotypes have been developed worldwide through cultivar screening and conventional breeding. Molecular markers are powerful in facilitating the selection of low-Cd cereal cultivars. Modern molecular breeding technologies may have great potential in breeding programs for the development of low-Cd cultivars, especially when coupled with conventional breeding. In this review, we provide a synthesis of low-Cd cereal breeding.

Breeding for low cadmium accumulation cereals / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Cadmium (Cd) is an element that is nonessential and extremely toxic to both plants and human beings. Soil contaminated with Cd has adverse impacts on crop yields and threatens human health via the food chain. Cultivation of low-Cd cultivars has been of particular interest and is one of the most cost-effective and promising approaches to minimize human dietary intake of Cd. Low-Cd crop cultivars should meet particular criteria, including acceptable yield and quality, and their edible parts should have Cd concentrations below maximum permissible concentrations for safe consumption, even when grown in Cd-contaminated soil. Several low-Cd cereal cultivars and genotypes have been developed worldwide through cultivar screening and conventional breeding. Molecular markers are powerful in facilitating the selection of low-Cd cereal cultivars. Modern molecular breeding technologies may have great potential in breeding programs for the development of low-Cd cultivars, especially when coupled with conventional breeding. In this review, we provide a synthesis of low-Cd cereal breeding.

Disentangling the genetic bases of Saccharomyces cerevisiae nitrogen consumption and adaptation to low nitrogen environments in wine fermentation

The budding yeast Saccharomyces cerevisiae has been considered for more than 20 years as a premier model organ- ism for biological sciences, also being the main microorganism used in wide industrial applications, like alcoholic fermentation in the winemaking process. Grape juice is a challenging environment for S. cerevisiae , with nitrogen deficiencies impairing fermentation rate and yeast biomass production, causing stuck or sluggish fermentations, thus generating sizeable economic losses for wine industry. In the present review, we summarize some recent efforts in the search of causative genes that account for yeast adaptation to low nitrogen environments, specially focused in wine fermentation conditions. We start presenting a brief perspective of yeast nitrogen utilization under wine fermentative conditions, highlighting yeast preference for some nitrogen sources above others. Then, we give an outlook of S. cerevisiae genetic diversity studies, paying special attention to efforts in genome sequencing for population structure determination and presenting QTL mapping as a powerful tool for phenotype-genotype correlations. Finally, we do a recapitulation of S. cerevisiae natural diversity related to low nitrogen adaptation, specially showing how different studies have left in evidence the central role of the TORC1 signalling pathway in nitrogen utilization and positioned wild S. cerevisiae strains as a reservoir of beneficial alleles with potential industrial applications (e.g. improvement of industrial yeasts for wine production). More studies focused in disentangling the genetic bases of S. cerevisiae adaptation in wine fermentation will be key to determine the domestication effects over low nitrogen adaptation, as well as to definitely proof that wild S. cerevisiae strains have potential genetic determinants for better adaptation to low nitrogen conditions.

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers

Abstract The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean.

Investigation of Splicing Quantitative Trait Loci in Arabidopsis thaliana

The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs.

Identificação de QTLS associados à resistência parcial à mancha branca do milho / Identification of partial resistance from QTLS to maize white spot

O milho é um dos cereais mais importantes cultivados no mundo, porém, fatores como as doenças podem ocasionar decréscimos no rendimento de grãos. A mancha branca, causada por um complexo de patógenos, está entre as principais doenças desta cultura e pode ocasionar perdas de cerca de 60 %. Dentro deste contexto, este trabalho teve como objetivos estimar parâmetros genéticos, identificar e mapear QTLs associados à resistência à mancha branca do milho, visando o desenvolvimento de genótipos resistentes à doença. Noventa e oito famílias F2:3 do cruzamento entre as linhagens BS01 (suscetível) e BS02 (resistente) e 90 famílias F2:3 do cruzamento entre BS03 (suscetível) e BS04 (resistente) foram conduzidas a campo em três ambientes. As herdabilidades variaram de 82,3 % a 86,2 % nos locais avaliados para a população 1. Para a população 2 a herdabilidade variou de 76 % a 86,6 %. Na análise conjunta para a resistência nas duas populações, efeitos entre pais e entre progênies foram significativos, assim como a interação de progênies e local, indicando que uma família superior em um local não será obrigatoriamente superior em outro local. Dos QTLs testados nas populações 1 e 2, foram encontrados marcadores que expressaram até 25% da variância fenotípica nos grupos de ligação 1, 3, 6 e 9. Assim, estes dados em conjunto demonstram a possibilidade de seleção assistida, para a resistência à mancha branca do milho, nas gerações iniciais com o uso dos marcadores moleculares estudados.

Maize is one of the most important cereal crops in the world; however, diseases, among other factors, may drastically reduce its grain yield. The white spot disease, caused by a complex of pathogens, is one of the most important syndromes affecting maize, causing losses of up to 60%. Thus, this study aimed to estimate heritability, to identify and to map QTLs associated with resistance to white spot in maize. Ninety-eight F2:3 families from a cross between lines BS01 (susceptible) and BS02 (resistant) and ninety F2:3 families from a cross between BS03 (susceptible) and BS04 (resistant) were evaluated in a lattice square (10x10) experimental design in three environments. Heritability estimations ranged from 82.3% to 86.2% in population 1, and from 76% to 86.6% in population 2. A joint analysis of both populations showed significant effects among parents and progenies, so it did for the interactions of locations and progenies. It means that a specific family may not show the same performance for resistance to white spot across different environments. QTLs for resistance to white spot were found in the linkage groups 1, 3, 6 and 9 in both populations. These QTLs explained up to 25% of the total phenotypic variation for the studied trait. Combined, these data confirm the possibility of marker assisted selection for resistance to maize white spot in early generations.

The genetic dissection of quantitative traits in crops

Most traits of interest in plant breeding show quantitative inheritance, which complicate the breeding process since phenotypic performances only partially reflects the genetic values of individuals. The genetic variation of a quantitative trait is assumed to be controlled by the collective effects of quantitative trait loci (QTLs), epistasis (interaction between QTLs), the environment, and interaction between QTL and environment. Exploiting molecular markers in breeding involve finding a subset of markers associated with one or more QTLs that regulate the expression of complex traits. Many QTL mapping studies conducted in the last two decades identified QTLs that generally explained a significant proportion of the phenotypic variance, and therefore, gave rise to an optimistic assessment of the prospects of markers assisted selection. Linkage analysis and association mapping are the two most commonly used methods for QTL mapping. This review provides an overview of the two QTL mapping methods, including mapping population type and size, phenotypic evaluation of the population, molecular profiling of either the entire or a subset of the population, marker-trait association analysis using different statistical methods and software as well as the future prospects of using markers in crop improvement.

Quantitative trait loci for carcass, internal organ and meat quality traits on porcine chromosomes 16, 17 and 18

The objective of this study was to map quantitative trait loci (QTL) on porcine chromosomes 16, 17 and 18 and to determine their association with carcass, organ and meat quality traits. An F2 population was produced by crossing two boars of the naturalized Brazilian Piau breed with 18 commercial females (Landrace x Large White x Pietrain). The population was genotyped for 11 microsatellite markers distributed over the three chromosomes and the results were used to construct a marker-specific linkage map for the population. Analysis of the polymorphic information content showed that the microsatellite markers were adequate for the study of quantitative traits. QTL were identified by regression interval mapping using QTL Express software. QTL not previously described in the literature were detected on chromosome 16, whereas QTL described in other populations were detected on chromosomes 17 and 18. The information from the significant QTL identified here will be useful for future fine-mapping studies and should provide a better understanding of productive phenotypes in pigs.

Mapping of quantitative trait loci and confirmation of the FAT1 region on chromosome 4 in an F2 population of pigs

The objective was to map QTL on porcine chromosome 4 and to associate them with carcass and internal organ traits in an F2 population. The F1 population was produced by outbreed crossing, using two native Brazilian breed Piau boars and 18 commercial sows. A total of 617 F2 animals issued from 11 F1 boars and 54 F1 sows were typed for a total of five microsatellite markers. The data were analyzed by multiple regressions developed for the analysis of crosses between outbred lines, using the QTL Express software. Significant evidence for QTL was found for pig chromosome 4 regarding carcass and internal organ traits. All QTL were detected in the same region of the chromosome, designated FAT1.