Introgression lines (ILs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action or interaction in theoretical studies. A set of 159 ILs carrying variant introgressed segments from Chinese common wild rice (Oryza rufipogon Griff.), collected from Dongxiang county, Jiangxi Province, in the background of Indica cultivar (Oryza sativa L.), Guichao 2, was developed using 126 polymorphic simple sequence repeats (SSR) loci. The 159 ILs represented 67.5% of the genome of O. rufipogon. All the ILs have the proportions of the recurrent parent ranging from 92.4 to 99.9%, with an average of 97.4%. The average proportion of the donor genome for the BC(4)F(4) population was about 2.2%. The mean numbers of homozygous and heterozygous donor segments were 2 (ranging 0-8) and 1 (ranging 0-7), respectively, and the majority of these segments had sizes less than 10 cM. QTL analysis was conducted based on evaluation of yield-related traits of the 159 ILs at two sites, in Beijing and Hainan. For 6 out of 17 QTLs identified at two sites corresponding to three traits (panicles per plant, grains per panicle and filled grains per plant, respectively), the QTLs derived from O. rufipogon were usually associated with an improvement of the target trait, although the overall phenotypic characters of O. rufipogon were inferior to that of the recurrent parent. Of the 17 QTLs, 5 specific QTLs strongly associated with more than one trait were observed. Further analysis of the high-yielding and low-yielding ILs revealed that the high-yielding ILs contained relatively less introgressed segments than the low-yielding ILs, and that the yield increase or decrease was mainly due to the number of grain. On the other hand, low-yielding ILs contained more negative QTLs or disharmonious interactions between QTLs which masked trait-enchancing QTLs. These ILs will be useful in identifying the traits of yield, tolerance to low temperature and drought stress, and detecting favorable genes of common wild rice.

Tonoplast transporters, including proton pumps and secondary transporters, are essential for plant cell function and for quality formation of fleshy fruits and ornamentals. Vacuolar transport of anthocyanins, malate, and other metabolites is directly or indirectly dependent on the H +-pumping activities of vacuolar H +-ATPase (VHA) and/or vacuolar H +-pyrophosphatase, but how these proton pumps are regulated in modulating vacuolar transport is largely unknown. Here, we report a transcription factor, MdMYB1, in apples that binds to the promoters of two genes encoding the B subunits of VHA, MdVHA-B1 and MdVHA-B2, to transcriptionally activate its expression, thereby enhancing VHA activity. A series of transgenic analyses in apples demonstrates that MdMYB1/10 controls cell pH and anthocyanin accumulation partially by regulating MdVHA-B1 and MdVHA-B2. Furthermore, several other direct target genes of MdMYB10 are identified, including MdVHA-E2, MdVHP1, MdMATE-LIKE1, and MdtDT, which are involved in H +-pumping or in the transport of anthocyanins and malates into vacuoles. Finally, we show that the mechanism by which MYB controls malate and anthocyanin accumulation in apples also operates in Arabidopsis (Arabidopsis thaliana). These findings provide novel insights into how MYB transcription factors directly modulate the vacuolar transport system in addition to anthocyanin biosynthesis, consequently controlling organ coloration and cell pH in plants.

A critical evolutionary step during rice domestication was the elimination of seed shattering. Wild rice disperses seeds freely at maturity to guarantee the propagation, while cultivated rice retains seeds on the straws to make easy harvest and decrease the loss of production. The molecular basis for this key event during rice domestication remains to be elucidated. Here we show that the seed shattering is controlled by a single dominant gene, Shattering1 (SHA1), encoding a member of the trihelix family of plant-specific transcription factors. SHA1 was mapped to a 5.5 kb genomic fragment, which contains a single open reading frame, using a backcrossed population between cultivated rice Teqing and an introgression line IL105 with the seed shattering habit derived from perennial common wild rice, YJCWR. The predicted amino acid sequence of SHA1 in YJCWR and IL105 is distinguished from that in eight domesticated rice cultivars, including Teqing, by only a single amino acid substitution (K79N) caused by a single nucleotide change (g237t). Further sequence verification on the g237t mutation site revealed that the g237t mutation is present in all the domesticated rice cultivars, including 92 indica and 108 japonica cultivars, but not in any of the 24 wild rice accessions examined. Our results demonstrate that the g237t mutation in SHA1 accounts for the elimination of seed shattering, and that all the domesticated rice cultivars harbor the mutant sha1 gene and therefore have lost the ability to shed their seeds at maturity. In addition, our data support the theory that the non-shattering trait selection during rice domestication occurred prior to the indica-japonica differentiation in rice evolutionary history.

Common wild rice (Oryza rufipogon), the wild relative of Asian cultivated rice (Oryza sativa), flaunts long, barbed awns, which are necessary for efficient propagation and dissemination of seeds. By contrast, O. sativa cultivars have been selected to be awnless or to harbor short, barbless awns, which facilitate seed processing and storage. The transition from long, barbed awns to short, barbless awns was a crucial event in rice domestication. Here, we show that the presence of long, barbed awns in wild rice is controlled by a major gene on chromosome 4, LONG AND BARBED AWN1 (LABA1), which encodes a cytokinin-activating enzyme. A frame-shift deletion in LABA1 of cultivated rice reduces the cytokinin concentration in awn primordia, disrupting barb formation and awn elongation. Sequencing analysis demonstrated low nucleotide diversity and a selective sweep encompassing an ;800-kb region around the derived laba1 allele in cultivated rice. Haplotype analysis revealed that the laba1 allele originated in the japonica subspecies and moved into the indica gene pool via introgression, suggesting that humans selected for this locus in early rice domestication. Identification of LABA1 provides new insights into rice domestication and also sheds light on the molecular mechanism underlying awn development.

Rice (Oryza sativa L.) is a staple food for more than half of the world's population. To meet the ever-increasing demand for food, because of population growth and improved living standards, world rice production needs to double by 2030. The development of new elite rice varieties with high yield and superior quality is challenging for traditional breeding approaches, and new strategies need to be developed. Here, we report the successful development of new elite varieties by pyramiding major genes that significantly contribute to grain quality and yield from three parents over five years. The new varieties exhibit higher yield potential and better grain quality than their parental varieties and the China's leading super-hybrid rice, Liang-you-pai-jiu (LYP9 or Pei-ai 64S/93-11). Our results demonstrate that rational design is a powerful strategy for meeting the challenges of future crop breeding, particularly in pyramiding multiple complex traits.

In present study, Fe, Zn, Mn, Cu, Ca, Mg, P and K contents of 85 introgression lines (ILs) derived from a cross between an elite indica cultivar Teqing and the wild rice (Oryza rufipogon) were measured by inductively coupled argon plasma (ICAP) spectrometry. Substantial variation was observed for all traits and most of the mineral elements were significantly positive correlated or independent except for Fe with Cu. A total of 31 putative quantitative trait loci (QTLs) were detected for these eight mineral elements by single point analysis. Wild rice (O. rufipogon) contributed favorable alleles for most of the QTLs (26 QTLs), and chromosomes 1, 9 and 12 exhibited 14 QTLs (45%) for these traits. One major effect of QTL for zinc content accounted for the largest proportion of phenotypic variation (11%-19%) was detected near the simple sequence repeats marker RM152 on chromosome 8. The co-locations of QTLs for some mineral elements observed in this mapping population suggested the relationship was at a molecular level among these traits and could be helpful for simultaneous improvement of these traits in rice grain by marker assisted selection.

Inflorescence architecture is a key agronomical factor determining grain yield, and thus has been a major target of cereal crop domestication. Transition from a spread panicle typical of ancestral wild rice (Oryza rufipogon Griff.) to the compact panicle of present cultivars (O. sativa L.) was a crucial event in rice domestication. Here we show that the spread panicle architecture of wild rice is controlled by a dominant gene, OsLG1, a previously reported SBP-domain transcription factor that controls rice ligule development. Association analysis indicates that a single-nucleotide polymorphism-6 in the OsLG1 regulatory region led to a compact panicle architecture in cultivars during rice domestication. We speculate that the cis-regulatory mutation can fine-tune the spatial expression of the target gene, and that selection of cis-regulatory mutations might be an efficient strategy for crop domestication.

Malate, the predominant organic acid in many fruits, is a crucial component of the organoleptic quality of fruit, including taste and flavor. The genetic and environmental mechanisms affecting malate metabolism in fruit cells have been studied extensively. However, the transcriptional regulation of malate-metabolizing enzymes and vacuolar transporters remains poorly understood. Our previous studies demonstrated that MdMYB1 modulates anthocyanin accumulation and vacuolar acidification by directly activating vacuolar transporters, including MdVHA-B1, MdVHA-E, MdVHP1 and MdtDT. Interestingly, we isolated and identified a MYB transcription factor, MdMYB73, a distant relative of MdMYB1 in this study. It was subsequently found that MdMYB73 protein bound directly to the promoters of MdALMT9 (aluminum-activated malate transporter 9), MdVHA-A (vacuolar ATPase subunit A) and MdVHP1 (vacuolar pyrophosphatase 1), transcriptionally activating their expression and thereby enhancing their activities. Analyses of transgenic apple calli demonstrated that MdMYB73 influenced malate accumulation and vacuolar pH. Furthermore, MdCIbHLH1 interacted with MdMYB73 and enhanced its activity upon downstream target genes. These findings help to elucidate how MdMYB73 directly modulates the vacuolar transport system to affect malate accumulation and vacuolar pH in apple.