Artificial selection for a green revolution gene during japonica rice domestication

Abstract

The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene, semi-dwarf1 (sd1), which encodes a gibberellin biosynthesis enzyme, made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we report that SD1 was involved not only in modern breeding including the green revolution, but also in early steps of rice domestication. We identified two SNPs in O. sativa subspecies (ssp.) japonica SD1 as functional nucleotide polymorphisms (FNPs) responsible for shorter culm length and low gibberellin biosynthetic activity. Genetic diversity analysis among O. sativa ssp. japonica and indica, along with their wild ancestor O. rufipogon Griff, revealed that these FNPs clearly differentiate the japonica landrace and O. rufipogon. We also found a dramatic reduction in nucleotide diversity around SD1 only in the japonica landrace, not in the indica landrace or O. rufipogon. These findings indicate that SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication, suggesting that ancient humans already used the green revolution gene.

Map-Based Cloning of qSD1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice

“…The allelic distribution was associated with the subspeciation of indica and japonica rice (Supplemental Fig. S3; Nagano et al, 2005;Asano et al, 2011). A discussion was focused on whether the nonrandom distribution arose from an artificial selection for reduced plant height early during the domestication of japonica rice (Asano et al, 2011;Paterson and Li, 2011).…”

“…In addition, the qSD1-2 region was reported for the semidwarf1 (sd1) gene, the plant height QTLs CULM LENGTH 1a (qCL1a), qCL1b, ph1, and qPH1, and the QTLs associated with root, seedling, and panicle growth, flowering time, and seed setting (Asano et al, 2011;Kovi et al, 2011;Mispan et al, 2013;Zhang et al, 2013). Thus, the objectives of this research were (1) to isolate the qSD1-2 underlying gene from the multi-QTL region and confirm its functions; (2) to identify the molecular and physiological mechanisms of dormancy development regulated by the cloned and confirmed gene; and (3) to determine the origin, distribution, and functional differentiation of major alleles at the seed dormancy locus.…”

Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia

“…However, this result may be caused by the extremely low diversity of DTH2 in cultivated and wild rice. As an alternative, we sequenced and calculated the diversity for the 20 genes surrounding DTH2, as selection might lead to a selective sweep in the flanking region of the target gene (20). As expected, the average nucleotide diversity of the 20 genes in japonica (π = 0.000263) is much lower than those of other rice groups (π = 0.0022 for indica, π = 0.0033 for javanica) and wild rice (π = 0.0043) (SI Appendix, Fig.…”

“…Recently, several genes associated with the domestication of cultivated rice have been cloned, including those controlling shattering (shattering4 and QTL of seed shattering in chromosome 1), pericarp color (Rc), plant architecture (PROS-TRATE GROWTH 1 and Semi-dwarf1), and seed dormancy (Seed dormancy 4) (15)(16)(17)(18)(19)(20)(21). Rice is a short-day (SD) plant but is cultivated in diverse environments at latitudes ranging from 55°N in China to 36°S in Chile, far beyond the geographical range of its wild progenitor, Oryza rufipogon (22).…”

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

“…Second, we simulated a 5-Mb genomic region across 30 accessions from one rice population, using the software SFS_CODE (Hernandez 2008). We assumed an effective population size of 125,000 (Caicedo et al 2007;Asano et al 2011), a mutation rate of 10 À8 (Caicedo et al 2007), a recombination rate of 4 cM/Mb (Tian et al 2009;Asano et al 2011), and two realistic self-pollinating rates of 0.7 and 0.95 (Oka 1988) ('-theta 0.005 -rho 0.02 -self [0.7,0.95] -sampSize 30'). We then used the program ART (Huang et al 2012b) to simulate 23 coverage 100-bp mapped reads with no indels directly in SAM format ('-len 100 -fcov 2 -ir 0 -dr 0 -ir2 0 -dr2 0 -qs 10 -qs2 10 -sam').…”