Photo shows the root morphology and plant type of the cassava variety, Rayong 1, which was selected and released by Rayong Field Crops Research Center, Department of Agriculture, Thailand in 1975. Rayong 1 has excellent agronomic traits and relatively high yield and thus, was used as a parent to breed Rayong 60 and KU50, which were later released in 1987 and 1992, respectively (This issue, p. 145–166).
(M. Ishitani: International Center for Tropical Agriculture (CIAT))
Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.
In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha–1 in 1996 to 21.3 t ha–1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.
Salinity causes major reductions in cultivated land area, crop productivity, and crop quality, and salt-tolerant crops have been required to sustain agriculture in salinized areas. The annual C4 crop plant Sorghum bicolor (L.) Moench is salt tolerant, with large variation among accessions. Sorghum’s salt tolerance is often evaluated during early growth, but such evaluations are weakly related to overall performance. Here, we evaluated salt tolerance of 415 sorghum accessions grown in saline soil (0, 50, 100, and 150 mM NaCl) for 3 months. Some accessions produced up to 400 g per plant of biomass and showed no growth inhibition at 50 mM NaCl. Our analysis indicated that the genetic factors that affected biomass production under 100 mM salt stress were more different from those without salt stress, comparing to the differences between those under 50 mM and 100 mM salt stress. A genome-wide association study for salt tolerance identified two single-nucleotide polymorphisms (SNPs) that were significantly associated with biomass production, only at 50 mM NaCl. Additionally, two SNPs were significantly associated with salt tolerance index as an indicator for growth response of each accession to salt stress. Our results offer candidate genetic resources and SNP markers for breeding salt-tolerant sorghum.
Humulus lupulus (2n = 2x = 20) as a source of hop resins, essential oils and polyphenols has value in brewing, pharmacy and cosmetology. Conventional crossing between tetraploids of ‘Sybilla’ and diploid males were performed to obtain F1 hybrids. Cytological studies revealed that 83.8% of the hybrids were triploids (2n = 3x = 30), 15.2% were aneuploids in which the chromosome number ranged from 28–32. Tetraploids (2n = 4x = 40) and diploids were also observed, which indicates numerous disturbances of gametogenesis of the parental forms. STS markers specific for male plants showed that females outnumbered male individuals among the F1 hybrids, which is in accordance with the distribution of sex ratio characteristic for diploid hybrids of H. lupulus. Female triploids were compared to the control ‘Sybilla’ with regard to their functional characteristics and alpha acids content in cones. A two year-long experiment showed that most of the triploids had a significantly higher position of fructiferous branches and shoot twist index compared to diploids of ‘Sybilla’. There was also a significantly extended time for them to reach technological maturity of cones. Triploids were distinguished by a significantly lower seed content compared to ‘Sybilla’, therefore the raw material obtained from them is more suitable for the production of hop pellets and extracts.
Maize rough dwarf disease (MRDD) is caused by viruses in the Fijivirus genus in the family Reoviridae. MRDD resistance can be improved by a combination of marker-assisted selection (MAS) and conventional breeding strategies. In our previous study, we fine-mapped a major QTL qMrdd8 and developed the functional Indel marker IDP25K. In the present study, qMrdd8 from the donor parent X178 was introgressed into elite inbred lines derived from the three corn heterotic groups using multi-generation backcrossing and MAS. Recipient lines included Huangzao4, Chang7-2, Ye478, Zheng58, Zhonghuang68, B73, and Ji846. Markers used for foreground selection included IDRQ4, IDRQ47, IDP25K, and IDP27K. Background selection was carried out in the BC3 or BC4 using 107 SSR markers to select lines with the highest rate of recovery of the particular recurrent parent genome. Plants from BC4F2 and BC3F2 that carried the shortest qMrdd8 interval from X178 and those with the highest rate of recovery of the recurrent parent genome were then selected to create converted homozygous inbred lines. In 2017, seven converted inbred lines and five hybrids exhibited enhanced resistance to MRDD, while other agronomic traits were not affected under nonpathogenic stress conditions. Thus, the MRDD resistance allele at the qMrdd8 locus, or IDP25K, should be valuable for maize breeding programs in China.
The optimization of heading date is a key aspect for maximizing grain productivity in cereal crops including rice. The combinations of genes for heading date, a quantitative trait, are a major driver in the wide adaptability of cultivated rice worldwide. Here, we identified a novel QTL, qDTH3 (quantitative trait locus for days-to-heading on chromosome 3), for early flowering time in the F2 population derived from a cross between Hoshinoyume (HS) and Daichinohoshi (DH) among local rice populations with extremely early heading date. The DH allele at qDTH3, qDTH3DH, headed 2.7 days earlier than the HS allele at qDTH3, qDTH3HS. We sought to design a genotype for earlier heading date by pyramiding of five heading date genes. We designated this aggregate of the five genes as DATTO5. Plants with DATTO5 were selected from the F2 population derived from a cross between DH and HShd5, which is a near-isogenic line carrying a loss-of-function of days to heading 8 in a genetic background of HS. Plants with DATTO5 exhibited earlier heading date but reduced fitness, including shorter culm and panicle length and fewer seeds compared with HS, as a representative local rice variety with extremely early heading date.
Citrus species are some of the most valuable and widely consumed fruits globally. The genome sequences of representative citrus (e.g., Citrus clementina, C. sinensis, C. grandis) species have been released but the research base for mandarin molecular breeding is still poor. We assembled the genomes of Citrus unshiu and Poncirus trifoliata, two important species for citrus industry in Japan, using hybrid de novo assembly of Illumina and PacBio sequence data, and developed the Mikan Genome Database (MiGD). The assembled genome sizes of C. unshiu and P. trifoliata are 346 and 292 Mb, respectively, similar to those of citrus species in public databases; they are predicted to possess 41,489 and 34,333 protein-coding genes in their draft genome sequences, with 9,642 and 8,377 specific genes when compared to C. clementina, respectively. MiGD is an integrated database of genome annotation, genetic diversity, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information, with these contents being mutually linked by genes. MiGD facilitates access to genome sequences of interest from previously reported linkage maps through CAPS markers and obtains polymorphism information through the multiple genome browser TASUKE. The genomic resources in MiGD (https://mikan.dna.affrc.go.jp) could provide valuable information for mandarin molecular breeding in Japan.
Zeaxanthin, a natural fat-soluble pigment, not only increases plant resistance, but also has vital significance for human health. However, quantitative trait loci (QTL) and the epistatic effects of zeaxanthin concentration in maize kernel have not been well studied. To identify QTLs and analyse the epistatic effects of zeaxanthin concentration in maize kernel, two sets of segregating generations derived from the cross between HuangC (a high zeaxanthin concentration inbred line) and Rezi1 (a low zeaxanthin concentration inbred line) were evaluated in three different environments. One major-effect QTL, qZea6a, explains 41.4–71.4% of the phenotypic variation and two QTLs, qZea4a and qZea3a, show LOD > 3 for zeaxanthin concentration detected over two generations and three different environments. Four of the ten QTL pairs show epistatic effects, explaining 7.34–14.3% of the phenotypic variance. Furthermore, additivity was the major allelic action at zeaxanthin concentration QTLs located in F2 and F2:3 populations and plants with homozygous HuangC alleles have a strong genetic ability in enhancing zeaxanthin concentration in maize kernel. These results will contribute to understanding these complex loci better and provide awareness about zeaxanthin concentration to maize breeders and scientists involved in maize research.
Burkholderia glumae causes bacterial seedling rot (BSR) and bacterial grain rot (BGR) in rice (Oryza sativa), both of which are important diseases in Japan. We previously evaluated major Japanese cultivars for BGR resistance and selected standard cultivars for resistance assessments. Here, we assessed the BSR occurrence rate in cultivars from the World Rice Collection (WRC) and other sources and found wide variation in resistance. Next, we evaluated major Japanese cultivars for BSR resistance and found that two Japanese landraces, ‘Kujuu’ and ‘Aikoku’, showed “strong” resistance; most others were categorized as “medium” or “medium to weak”. We previously developed a near-isogenic line (RBG1-NIL) by introducing the genomic region containing RBG1, a quantitative trait locus (QTL) for BSR resistance, from ‘Nona Bokra’ (indica) into ‘Koshihikari’ (temperatejaponica). The resistance level of RBG1-NIL was “strong”, indicating the effectiveness of RBG1 against BSR. The correlation between BSR and BGR resistance scores was low, indicating that it is necessary to introduce QTLs for resistance from different sources to develop cultivars resistant to both BSR and BGR. On the basis of the screening results, we selected standard cultivars for BSR resistance to cover a range of resistance levels.
In this study, DNA markers were developed for discrimination of strawberry (Fragaria × ananassa L.) cultivars based on retrotransposon insertion polymorphisms. We performed a comprehensive genomic search to identify retrotransposon insertion sites and subsequently selected one retrotransposon family, designated CL3, which provided reliable discrimination among strawberry cultivars. Through analyses of 75 strawberry cultivars, we developed eight cultivar-specific markers based on CL3 retrotransposon insertion sites. Used in combination with 10 additional polymorphic markers, we differentiated 35 strawberry cultivars commonly cultivated in Japan. In addition, we demonstrated that the retrotransposon-based markers were effective for PCR detection of DNA extracted from processed food materials, whereas a SSR marker was ineffective. These results indicated that the retrotransposon-based markers are useful for cultivar discrimination for processed food products, such as jams, in which DNA may be fragmented or degraded.
In this study, the chromosome number and composition of a novel perennial forage crop, ‘Yucao No. 6’ (Yu6), was revealed by chromosome spread and McGISH (multicolor genomic in situ hybridization) techniques to clarify its genitor origin. Cytogenetic analysis showed that Yu6, which has 56 chromosomes, is an aneuploid representing 12, 17 and 27 chromosomes from Zea mays ssp. mays L. (Zm, 2n = 2x = 20), Tripsacum dactyloides L. (Td, 2n = 4x = 72), and Z. perennis (Hitchc.) Reeves & Mangelsd. (Zp, 2n = 4x = 40), respectively. This finding indicates that Yu6 is the product of a reduced egg (n = 36 = 12Zm + 17Td + 7Zp) of MTP (a near-allohexaploid hybrid, 2n = 74 = 20Zm + 34Td + 20Zp) fertilized by a haploid sperm nucleus (n = 20Zp) of Z. perennis. Moreover, 3 translocated chromosomes consisting of the maize-genome chromosome with the segment of Z. perennis were observed. These results suggest that it is practical to develop perennial forage maize by remodeling the chromosomal architecture of MTP offspring with Z. perennis as a pollen parent. Finally, the overview of forage breeding in the Zea and Tripsacum genera was discussed.
Speckled snow mold caused by Typhula ishikariensis is one of the most devastating diseases of winter wheat in Hokkaido, Japan and parts of the Pacific Northwest region of USA. Münstertaler is a winter wheat landrace from Switzerland that has very high resistance to snow mold and superior freezing tolerance. Quantitative trait loci (QTL) for resistance to speckled snow mold were identified in a doubled haploid population derived from a cross between Münstertaler and susceptible variety Ibis, both under field conditions and controlled environment tests. Composite interval mapping analysis revealed a major QTL on chromosome 5D from Münstertaler, and on chromosome 6B from Ibis. Flanking microsatellite marker cfd 29 for the QTL on chromosome 5D was about 5 cM distant from vernalization requirement gene Vrn-D1, suggesting that the QTL on chromosome 5D is located on a cold-stress-related gene cluster along with Vrn-D1 and freezing tolerance gene Fr-D1. The QTL on chromosome 6B from Ibis was located on the centromere region flanking QTn.mst-6B, which is reported to increase plant tiller number.