Mathias Lorieux

Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations

A maximum-likelihood approach is used in order to estimate recombination fractions between markers showing segregation distortion in backcross populations. It is assumed that the distortions are induced by viability differences between gametes or zygotes due to one or more selected genes. We show that Baileys (1949) estimate stays consistent and efficient under more general assumptions than those defined by its author. This estimate should therefore be used instead of the classical maximum-likelihood estimate. The question of detection of linkage is also discussed. We show that the order of markers on linkage groups may be affected by segregation distortion.

MapDisto: fast and efficient computation of genetic linkage maps

Several options are available to the scientific community for genetic map construction but few are simple to install and use. Available programs either lack intuitive interface or are commercial, expensive for many laboratories. We present MapDisto, a free, user-friendly and powerful program for constructing genetic maps from experimental segregating populations. MapDisto is freely available at http://mapdisto.free.fr/DL/. Current version: 1.7.5.

Aroma in rice: genetic analysis of a quantitative trait

A new approach was developed which succeeded in tagging for the first time a major gene and two QTLs controlling grain aroma in rice. It involved a combination of two techniques, quantification of volatile compounds in the cooking water by gas chromatography, and molecular marker mapping. Four types of molecular marker were used (RFLPs, RAPDs, STSs, isozymes). Evaluation and mapping were performed on a doubled haploid line population which (1) conferred a precise character evaluation by enabling the analysis of large quantities of grains per genotype and (2) made possible the comparison of gas chromatography results and sensitive tests. The population size (135 lines) provided a good mapping precision. Several markers on chromosome 8 were found to be closely linked to a major gene controlling the presence of 2-acetyl-1-pyrroline (AcPy), the main compound of rice aroma. Moreover, our results showed that AcPy concentration in plants is regulated by at least two chromosomal regions. Estimations of recombination fractions on chromosome 8 were corrected for strong segregation distortion. This study confirms that AcPy is the major component of aroma. Use of the markers linked to AcPy major gene and QTLs for marker-assisted selection by successive backcrosses may be envisaged.

Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice

Abstract Rice is often found as various weedy forms in temperate or newly cultivated rice growing regions throughout the world. The emergence of these forms in the absence of true wild rice remains unclear. A genetic analysis of domestication-related traits (weed syndrome) has been conducted to better understand the appearance of these plants in rice fields. A doubled haploid (DH) population was derived from a cross between a japonica variety and a weedy plant collected in Camargue (France) to set up a genetic linkage map consisting of 68 SSR and 31 AFLP loci. Five qualitative traits related to pigmentation of different organs and 15 developmental and morphological quantitative traits were scored for genes and QTLs mapping. Despite a good reactivity in anther culture and a high fertility of the DH lines, segregation distortions were observed on chromosomal segments bearing gametophytic and sterility genes and corresponded to various QTLs evidenced in indica×japonica distant crosses. Mapping of the coloration genes was found to be in agreement with the presence of several genes previously identified and according to the genetic model governing the synthesis and distribution of anthocyan pigment in the plant. In addition, the main specific traits of weedy forms revealed the same genes/QTLs as progeny derived from a cross between Oryza sativa and its wild progenitor O. rufipogon. A large variation for most characters was found in the DH population, including transgressive variation. Significant correlations were observed between morphology and traits related to weeds and corresponded to a distinct colocalization of most of the QTLs on a limited number of chromosomal regions. The significance of these results on the origin of weedy forms and the de-domestication process is discussed.

A first interspecific Oryza sativa × Oryza glaberrima microsatellite-based genetic linkage map.

Abstract Oryza glaberrima is an endemic African cultivated rice species. To provide a tool for evaluation and utilisation of the potential of O. glaberrima in rice breeding, we developed an interspecific O. glaberrima×Oryza sativa genetic linkage map. It was based on PCR markers, essentially microsatellites and STSs. Segregation of markers was examined in a backcross (O. sativa/O. glaberrima//O. sativa) population. Several traits were measured on the BC1 plants, and major genes and QTLs were mapped for these traits. Several of these genes correspond well to previously identified loci. The overall map length was comparable to those observed in indica×japonica crosses, indicating that recombination between the two species occurs without limitation. However, three chromosomes show discrepancies with the indica×japonica maps. The colinearity with intraspecific maps was very good, confirming previous cytological observations. A strong segregation-distortion hot spot was observed on chromosome 6 near the waxy gene, indicating the presence of s10, a sporo-gametophytic sterility gene previously identified by Sano (1990). The main interests of such a PCR-based map for African rice breeding are discussed, including gene and QTL localisation, marker-assisted selection, and the development of interspecific introgression lines.

Genetic basis and mapping of the resistance to rice yellow mottle virus. I. QTLs identification and relationship between resistance and plant morphology

Abstract Rice yellow mottle virus (RYMV) resistance QTLs were mapped in a doubled-haploid population of rice, ‘IR64/Azucena’. Disease impact on plant morphology and development, expression of symptoms and virus content were evaluated in field conditions. Virus content was also assessed in a growth chamber. RYMV resistance was found to be under a polygenic determinism, and 15 QTLs were detected on seven chromosomal fragments. For all of the resistance QTLs detected, the favourable allele was provided by the resistant parent ‘Azucena’. Three regions were determined using different resistance parameters and in two environments. On chromosome 12, a QTL of resistance that had already been detected in this population and another indica/japonica population was confirmed both in the field and under controlled conditions. Significant correlations were observed between resistance and tillering ability, as measured on control non-inoculated plants. In addition, the three genomic fragments involved in resistance were also involved in plant architecture and development. In particular, the semi-dwarfing gene sd-1, on chromosome 1, provided by the susceptible parent, ‘IR64’, mapped in a region where resistance QTLs were detected with most of the resistance parameters. In contrast, the QTL of resistance mapped on chromosome 12 was found to be independent of plant morphology.

Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library

To organize data resulting from the phenotypic characterization of a library of 30 000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13 928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13 928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB.

First steps towards a rational use of African rice, Oryza glaberrima, in rice breeding through a 'contig line' concept.

In the past, utilisation of African cultivated rice, Oryza glaberrima, in O. sativa breeding was hampered by high sterility in interspecific F1 and in early progenies. Recent development of mapped molecular markers provides the opportunity to rationalise and to monitor introgressions between the two cultivated rice species. Development of such introgressed lines through interspecific hybridisation and backcrossing represents high potential to create new genetic and transgressive variation. We are initiating an original marker-aided backcross program with the aim of producing a set of 100 ‘contig lines’, each one bearing an alien O. glaberrima chromosomal fragment of around 20 cM in the O. sativa genetic background. As a preliminary step, we are now developing a genetic linkage map based on STS and RAPD markers, using an interspecific backcross between O. sativa and O. glaberrima. BC1 plants will then be selected to expedite the production of ‘contig lines’ exhibiting only the target fragment. The interspecific polymorphism is anticipated to be large enough to make this methodology feasible. Many advantages are expected from this approach, such as: (i) systematic assessment of the useful genetic resources displayed by O. glaberrima, (ii) improved and simplified detection of QTLs and (iii) comparative analysis of genomic organisation of O. glaberrima vs. O. sativa. Current work on evaluation of STS and RAPD polymorphism between parents and development of the BC1 population is presented.

A major quantitative trait locus for rice yellow mottle virus resistance maps to a cluster of blast resistance genes on chromosome 12.

ABSTRACT Two doubled-haploid rice populations, IR64/Azucena and IRAT177/ Apura, were used to identify markers linked to rice yellow mottle virus (RYMV) resistance using core restriction fragment length polymorphism (RFLP) maps. Resistance was measured by mechanical inoculation of 19-day-old seedlings followed by assessment of virus content by enzyme-linked immunosorbent assay tests 15 days after inoculation. IR64/Azucena and IRAT177/Apura populations, 72 and 43 lines, respectively, were evaluated, and resistance was found to be polygenic. Resistance was expressed as a slower virus multiplication, low symptom expression, and limited yield loss when assessed at the field level. Bulked segregant analysis using the IR64/Azucena population identified a single random amplified polymorphic DNA marker that mapped on chromosome 12 and corresponded to a major quantitative trait locus (QTL) evidenced by interval mapping. When pooling RFLP data, integrated mapping of this chromosome revealed that the QTL was common to the two populations and corresponded to a small chromosomal segment known to contain a cluster of major blast resistance genes. This region of the genome also reflected the differentiation observed at the RFLP level between the subspecies indica and japonica of Oryza sativa. This is consistent with the observation that most sources of RYMV resistance used in rice breeding are found in upland rice varieties that typically belong to the japonica subspecies.

A Genetic Model for the Female Sterility Barrier Between Asian and African Cultivated Rice Species

S1 is the most important locus acting as a reproductive barrier between Oryza sativa and O. glaberrima. It is a complex locus, with factors that may affect male and female fertility separately. Recently, the component causing the allelic elimination of pollen was fine mapped. However, the position and nature of the component causing female sterility remains unknown. To fine map the factor of the S1 locus affecting female fertility, we developed a mapping approach based on the evaluation of the degree of female transmission ratio distortion (fTRD) of markers. Through implementing this methodology in four O. sativa × O. glaberrima crosses, the female component of the S1 locus was mapped into a 27.8-kb (O. sativa) and 50.3-kb (O. glaberrima) region included within the interval bearing the male component of the locus. Moreover, evidence of additional factors interacting with S1 was also found. In light of the available data, a model where incompatibilities in epistatic interactions between S1 and the additional factors are the cause of the female sterility barrier between O. sativa and O. glaberrima was developed to explain the female sterility and the TRD mediated by S1. According to our model, the recombination ratio and allelic combinations between these factors would determine the final allelic frequencies observed for a given cross.