Pham Thien Thanh

OsLG1 regulates a closed panicle trait in domesticated rice

Reduction in seed shattering was an important phenotypic change during cereal domestication. Here we show that a simple morphological change in rice panicle shape, controlled by the SPR3 locus, has a large impact on seed-shedding and pollinating behaviors. In the wild genetic background of rice, we found that plants with a cultivated-like type of closed panicle had significantly reduced seed shedding through seed retention. In addition, the long awns in closed panicles disturbed the free exposure of anthers and stigmas on the flowering spikelets, resulting in a significant reduction of the outcrossing rate. We localized the SPR3 locus to a 9.3-kb genomic region, and our complementation tests suggest that this region regulates the liguleless gene (OsLG1). Sequencing analysis identified reduced nucleotide diversity and a selective sweep at the SPR3 locus in cultivated rice. Our results suggest that a closed panicle was a selected trait during rice domestication.

Molecular Genetic Analysis of Domestication Traits in Emmer Wheat. I: Map Construction and QTL Analysis using an F2 Pupulation

ABSTRACT Emmer wheat (Triticum turgidum ssp. dicoccum) was a principal crop in the development and spread of Neolithic agriculture in the Old World. It represents the primitive situation in the domestication of AABB tetraploid wheat. To understand the genetic modifications underlying the early stage of tetraploid wheat domestication, QTL analysis was carried out using 144 F2 plants derived from a cross between the domesticated emmer wheat and the wild emmer wheat (T. turgidum ssp. dicoccoides). To our knowledge, this is the first report of molecular linkage map and QTL analysis of the domestication-related characters in emmer wheat. The linkage map with a total length of 2849.8 cM was constructed using 227 microsatellite (SSR) markers. Chromosomal location and effect of QTLs were estimated for ten domestication-related traits including whole plant and spike characteristics. Seventeen QTLs were detected on chromosomes 1B, 2A, 2B, 3A, 3B, 4A, 5B, and 7B. Two regions on chromosomes 2A and 3B have a large effect on rachis fragility. The estimated locations of these QTLs corresponded to those of the Br genes identified in the previous studies on a more adapted durum wheat (T. turgidum ssp. turgidum conv. durum). Our results indicate that selection and conversion of at least two Br loci (on chromosomes 2A and 3B) occurred during the domestication of emmer wheat prior to appearance of free-threshing wheat (e.g. durum). The map positions of nine QTLs for the traits related to seed production overlapped in two regions on chromosomes 2A and 5B. The result suggests that these chromosomal regions played an important role in increasing seed production during the domestication of emmer wheat.

Gene interaction at seed-awning loci in the genetic background of wild rice

Seed awning is one of the important traits for successful propagation in wild rice. During the domestication of rice by ancient humans, plants with awnless seeds may have been selected because long awns hindered collection and handling activities. To investigate domestication of awnless rice, QTL analysis for seed awning was first carried out using backcross recombinant inbred lines between Oryza sativa Nipponbare (recurrent parent) and O. rufipogon W630 (donor parent). Two strong QTLs were detected in the same regions as known major seed-awning loci, An-1 and RAE2. Subsequent causal mutation surveying and fine mapping confirmed that O. rufipogon W630 has functional alleles at both loci. The gene effects and interactions at these loci were examined using two backcross populations with reciprocal genetic backgrounds of O. sativa Nipponbare and O. rufipogon W630. As awn length in wild rice varied among seeds even in the same plant, awn length was measured based on spikelet position. In the genetic background of cultivated rice, the wild alleles at An-1 and RAE2 had awning effects, and plants having both wild homozygous alleles produced awns whose length was about 70% of those of the wild parent. On the other hand, in the genetic background of wild rice, the substitution of cultivated alleles at An-1 and RAE2 contributed little to awn length reduction. These results indicate that the domestication process of awnless seeds was complicated because many genes are involved in awn formation in wild rice.