Yuchun Rao

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

Significance Hybrid rice developed in China has been contributing greatly to the world’s food production. The pioneer super hybrid rice developed by crossing 93–11 and Peiai 64s, Liang–You–Pei–Jiu has been widely grown in China and other Asia-Pacific regions for its high yield. Here, the quality genome sequences for both parental lines were presented and updated, and a high-resolution map of genome-wide graphic genotypes was constructed by deep resequencing a core population of 132 Liang–You–Pei–Jiu recombinant inbred lines. A series of yield-associated loci were fine-mapped, and two of them were delimited to regions each covering one candidate gene with the large recombinant inbred line population. The study provided an ideal platform for molecular breeding by quantitative trait loci cloning in rice. The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang–You–Pei–Jiu, the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93–11 and maternal cultivar PA64s of Liang–You–Pei–Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1, and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice.

SMALL GRAIN 1, which encodes a mitogen-activated protein kinase kinase 4, influences grain size in rice.

Although grain size is one of the most important components of grain yield, little information is known about the mechanisms that determine final grain size in crops. Here we characterize rice small grain1 (smg1) mutants, which exhibit small and light grains, dense and erect panicles and comparatively slightly shorter plants. The short grain and panicle phenotypes of smg1 mutants are caused by a defect in cell proliferation. The smg1 mutations were identified, using a map-based cloning approach, in mitogen-activated protein kinase kinase 4 (OsMKK4). Relatively higher expression of OsMKK4/SMG1 was detected in younger organs than in older ones, consistent with its role in cell proliferation. Green fluorescent protein (GFP)-OsMKK4/SMG1 fusion proteins appear to be distributed ubiquitously in plant cells. Further results revealed that OsMKK4 influenced brassinosteroid (BR) responses and the expression of BR-related genes. Thus, our findings have identified OsMKK4 as a factor for grain size, and suggest a possible link between the MAPK pathways and BRs in grain growth.

LSCHL4 from Japonica Cultivar, Which Is Allelic to NAL1, Increases Yield of Indica Super Rice 93-11

SUMMARY The basic premise of high yield in rice is to improve leaf photosynthetic efficiency, and coordinate the source–sink relationship in rice plants. The quantitative trait loci (QTLs) qLSCHL4, japonica NAL1 allele from Nipponbare has a pleiotropic function, effectively increased leaf chlorophyll content, enlarged flag leaf size, and enhanced the yield of indica rice cultivar.

Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.)

In this study, one major QTL affecting gel consistency (GC) of japonica/indica cross was identified on chromosome 6 using a DH population. To understand the molecular mechanism that regulates GC in rice grains, the major QTL (qGC-6) was isolated through a map-based cloning approach utilizing chromosome segment substitution lines (CSSLs). Using 64 plants with extremely soft GC that were selected on recombinant break points between two SSR markers, RM540 and RM8200 in a BC4F2 population, qGC-6 was mapped to a 60-kb DNA region between two STS markers, S26 and S27. These two markers were then used to further identify recombination break points. Finally, qGC-6 was delimited in an interval of a 11-kb region. Gene prediction analysis of the 11-kb DNA sequence containing qGC-6 identified only one putative ORF, which encodes granule-bound starch synthesis protein (Wx protein). Results of sequencing analysis and complementation experiment confirmed that this candidate ORF is responsible for rice GC. Genetic evidences revealed that Wx might contribute equally to the grain amylose content-controlling gene as well as gel consistency. This new information is important to breed rice varieties with improved grain quality.

The pleiotropic ABNORMAL FLOWER AND DWARF1 affects plant height, floral development and grain yield in rice

Abstract Moderate plant height and successful establishment of reproductive organs play pivotal roles in rice grain production. The molecular mechanism that controls the two aspects remains unclear in rice. In the present study, we characterized a rice gene, ABNORMAL FLOWER AND DWARF1 (AFD1) that determined plant height, floral development and grain yield. The afd1 mutant showed variable defects including the dwarfism, long panicle, low seed setting and reduced grain yield. In addition, abnormal floral organs were also observed in the afd1 mutant including slender and thick hulls, and hull‐like lodicules. AFD1 encoded a DUF640 domain protein and was expressed in all tested tissues and organs. Subcellular localization showed AFD1‐green fluorescent fusion protein (GFP) was localized in the nucleus. Meantime, our results suggested that AFD1 regulated the expression of cell division and expansion related genes.

Rational design of high-yield and superior-quality rice

Rice (Oryza sativa L.) is a staple food for more than half of the worlds population. To meet the ever-increasing demand for food, because of population growth and improved living standards, world rice production needs to double by 20301. 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 Chinas 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.

PGL, encoding chlorophyllide a oxygenase 1, impacts leaf senescence and indirectly affects grain yield and quality in rice

Highlight PGL encodes CAO1 in rice, which is essential for Chl b synthesis and affects Chl synthesis and degradation. PGL also impacts leaf senescence and indirectly affects grain yield and quality.

EARLY SENESCENCE1 Encodes a SCAR-LIKE PROTEIN2 That Affects Water Loss in Rice

An actin nucleation protein affects water loss by regulating stomatal density. The global problem of drought threatens agricultural production and constrains the development of sustainable agricultural practices. In plants, excessive water loss causes drought stress and induces early senescence. In this study, we isolated a rice (Oryza sativa) mutant, designated as early senescence1 (es1), which exhibits early leaf senescence. The es1-1 leaves undergo water loss at the seedling stage (as reflected by whitening of the leaf margin and wilting) and display early senescence at the three-leaf stage. We used map-based cloning to identify ES1, which encodes a SCAR-LIKE PROTEIN2, a component of the suppressor of cAMP receptor/Wiskott-Aldrich syndrome protein family verprolin-homologous complex involved in actin polymerization and function. The es1-1 mutants exhibited significantly higher stomatal density. This resulted in excessive water loss and accelerated water flow in es1-1, also enhancing the water absorption capacity of the roots and the water transport capacity of the stems as well as promoting the in vivo enrichment of metal ions cotransported with water. The expression of ES1 is higher in the leaves and leaf sheaths than in other tissues, consistent with its role in controlling water loss from leaves. GREEN FLUORESCENT PROTEIN-ES1 fusion proteins were ubiquitously distributed in the cytoplasm of plant cells. Collectively, our data suggest that ES1 is important for regulating water loss in rice.

Regulatory Role of OsMADS34 in the Determination of Glumes Fate, Grain Yield, and Quality in Rice

Grasses produce seeds on spikelets, a unique type of inflorescence. Despite the importance of grass crops for food, the genetic mechanisms that control spikelet development remain poorly understood. In this study, we used m34-z, a new mutant allele of the rice (Oryza sativa) E-class gene OsMADS34, to examine OsMADS34 function in determining the identities of glumes (rudimentary glume and sterile lemma) and grain size. In the m34-z mutant, both the rudimentary glume and sterile lemma were homeotically converted to the lemma-like organ and acquired the lemma identity, suggesting that OsMADS34 plays important roles in the development of glumes. In the m34-z mutant, most of the grains from the secondary panicle branches (spb) were decreased in size, compared with grains from wild-type, but no differences were observed in the grains from the primary panicle branches. The amylose content and gel consistency, and a seed-setting rate from the spb were reduced in the m34-z mutant. Interesting, transcriptional activity analysis revealed that OsMADS34 protein was a transcription repressor and it may influence grain yield by suppressing the expressions of BG1, GW8, GW2, and GL7 in the m34-z mutant. These findings revealed that OsMADS34 largely affects grain yield by affecting the size of grains from the secondary branches.

A Simple Method for Preparation of Rice Genomic DNA

The extraction of DNA is often the most time consuming and laborious step in high-throughput molecular genetic analysis and marker assisted selection (MAS) programs. A simple method for preparation of rice genomic DNA was developed. A small amount (1-50 mg) of leaf tissue of rice seedling, 500 μL of extraction buffer, and one steel bead were put into a 2-mL microcentrifuge tube. After vigorously mashing for 2 min, 5 μL of supernatant was directly applied to PCR amplification. Otherwise, the supernatant was precipitated with two times volume of ethanol to obtain high quality genomic DNA. This method is simple, rapid, low cost, and reliable for PCR analysis. One person can manipulate as many as 96 samples for PCR in 10 min. It is especially suitable for genotyping of large number of samples.