Breeding Science最新文献

Polyphenol oxidase (PPO) is a key enzyme contributing to the time-dependent discoloration of wheat products. Developing cultivars with low PPO activity is one way to solve this problem. In this study, we focused on the Ppo-D1 gene, which has the second highest effect on grain PPO activity after the Ppo-A1 gene. Utilizing resequencing data, we found that the Ppo-D1 gene in the common wheat line 'Fukuhonoka-NIL', which exhibits low PPO activity, has an approximately 3 kb deletion in the 3'UTR and a 73 bp deletion in the third exon. The deletion in the third exon indicated that this allele was the ppo-D1d allele, previously identified in the wheat D genome progenitor, Aegilops tauschii Coss. Additionally, the ppo-D1d allele in 'Fukuhonoka-NIL' had very low expression, suggesting that this allele is non-functional. We developed a new co-dominant DNA marker for distinguishing the Ppo-D1a, Ppo-D1b and ppo-D1d alleles and demonstrated that F₂ plants homozygous for the ppo-D1d allele exhibited significantly lower grain PPO activity. Additionally, we determined that the ppo-D1d allele likely originated from Ae. tauschii ssp. tauschii (lineage 1) accessions. The ppo-D1d allele has not previously been found in common wheat (Triticum aestivum L., AABBDD genome), and thus the DNA marker developed in this study will be helpful for introducing this allele in common wheat breeding programs.

"Tanpo", a Japanese rice landrace widely cultivated approximately 120 years ago in Akita Prefecture, exhibits a shorter, wider, thicker, and heavier grain compared to Akitakomachi. Microscopic analysis has revealed that the epidermal cells of Tanpo spikelet hulls are narrower and shorter, with an increased number of cells in the grain width direction, thus resulting in a distinctive grain shape. In a genetic analysis of an F₂ population derived from a cross between Tanpo and Akitakomachi, the Tanpo GW5 allele was found to determine the grain shape in a recessive manner. The GW5 allele in Tanpo is a loss-of-function allele because it generates a stop codon immediately after the start codon with a 100-bp deletion within the first exon. Because the GW5 protein suppresses glycogen synthase kinase 2 (GSK2), a negative regulator of brassinosteroid (BR) signaling, GW5 deficiency in Tanpo results in reduced BR signaling. As a result, the expansion of epidermal cells was suppressed, while the radial cell division was promoted, which led to thicker and shorter spikelet hulls and, ultimately, the characteristic grain shape of Tanpo. The identification of this unique allele in the Tanpo landrace provides a valuable resource for breeding new rice varieties with unique grain characteristics.

Grain chalkiness decreases the appearance quality (APQ) of rice (Oryza sativa L.) grains and reduces consumer satisfaction. Improving APQ is a crucial issue for both marketing and breeding. Here, we screened chromosome segment substitution lines (CSSLs) with higher APQ to find promising genetic resources. These CSSLs harbor chromosome segments derived from multiple donors in the genetic background of 'Koshihikari', a leading japonica rice cultivar in Japan. Three CSSLs had an increased percentage of perfect grains without panicle weight loss under field conditions across 3 years in Tsukuba city, Ibaraki prefecture, Japan. The positions of reduced chalkiness in grains differed among CSSLs, suggesting the different contribution of the harbored chromosome segments to APQ improvement. There were no significant differences in days to heading, culm length, panicle length, or panicle number in all three CSSLs, but 1000-grain weight was reduced in one. These results identify two promising genetic resources for further improvement of APQ in current japonica cultivars with reduced chalkiness but unaltered heading date and yield traits.

Japanese red or white common bean (Phaseolus vulgaris L.) cultivars, used to make sweetened boiled beans, are called "kintoki" beans. Kintoki beans are planted to precede winter wheat for crop rotation in Hokkaido, northern Japan. Therefore, early maturity is an important trait for them. The aim of this study was to map the genomic region associated with days to maturity in kintoki beans by genome-wide association study (GWAS). Significant single nucleotide polymorphisms associated with days to maturity were detected on chromosome 1 (Pv01) by GWAS in 3 years, and the candidate region for early maturity was mapped to a 473-kb region. Sequencing analysis indicated that Phvul.001G221100, a phytochrome A3 gene, is likely to be responsible for early maturity in kintoki cultivars: the insertion of a cytosine in exon 1 at position 47 644 850 on Pv01 causes a frameshift that creates an early stop codon. Our findings suggest that the loss-of-function mutation of Phvul.001G221100 is derived from a leading cultivar, 'Taisho-Kintoki', and is originated from a spontaneous mutation in the oldest kintoki cultivar, 'Hon-Kintoki'. The DNA markers targeting the functional insertion of phytochrome A3 will be useful for marker-assisted selection in kintoki bean breeding.

Cassava is an important staple crop in tropical and subtropical regions. Cassava mosaic disease (CMD) is one of the most dangerous diseases affecting cassava production in Africa. Since the first reported in Southeast Asia in 2015, the CMD prevalence has become a concern in Southeast Asia. To combat it, CMD resistance has been introduced from African cassava into Asian elite cultivars. However, efficient DNA markers for the selection of CMD resistance are not available. The CMD2 locus confers resistance to African cassava mosaic virus via non-synonymous substitutions in the DNA polymerase δ subunit 1 gene (MePOLD1). Here, we developed DNA markers to identify the mutations providing the resistance. We examined the association between the resistance score in CMD-infected fields and the genotypes of hybrids of CMD-resistant and ‑susceptible Asian lines. Our study provides powerful tools to the global cassava breeding community for selecting CMD resistant cassava.

In barley (Hordeum vulgare L.), many DNA markers have been developed for the selection of traits related to various end-use purposes of breeding. To perform rapid marker-assisted selection of many lines, we developed Kompetitive Allele-Specific PCR (KASP) markers, which can be used for effective automatic genotyping of single nucleotide polymorphisms (SNPs). The KASP primers were designed for 17 SNPs in 14 genes related to important traits. The target allele of all primers tried was identified on the basis of high FAM fluorescence in comparison with that of HEX. To evaluate the suitability of the developed markers in breeding programs, we used them to genotype 62 representative cultivars and lines. Then, using six of the developed markers, we comprehensively analyzed a total of 2,941 lines collected from eight breeding sites with a genotyping success rate of 95.1%-99.8% (mean, 98.6%). All six markers showed differences in allele percentages among breeding programs, and specific allele combinations were observed in all four barley types. Our data will be useful for predicting phenotype segregation and designing cross combinations. The developed KASP marker set can be used for high-throughput genotyping and should make breeding more efficient when combined with an accelerated generation technique.

Strong yellow color, caused by carotenoid accumulation, in semolina flour made from durum wheat (Triticum turgidum L. subsp. durum (Desf.)) is one of the most important traits for pasta production. The first step in the carotenoid biosynthesis pathway, which is catalyzed by phytoene synthase (PSY), is a bottleneck, and allelic variation of Psy-A1 in durum wheat produces different yellow pigment contents (YPC) in seeds. Durum wheat carrying leaf rust resistance gene Lr19, which was translocated from wheat relative Thinopyrum ponticum chromosome 7E to durum wheat chromosome 7A, is known to produce high YPC, and the causal gene is presumed to be Psy-E1, which is tightly linked to Lr19. In this study, Psy-E1 produced higher YPC than Psy-A1 alleles, such as Psy-A1k, Psy-A1l and Psy-A1o, in durum wheat. Segregation analysis demonstrated that Psy-E1 is located at the Psy-A1 locus on chromosome 7A. In a 2-year field test of near-isogenic materials, Psy-E1 was accompanied by yield loss with decreases in grain number per spike, test weight and thousand-kernel weight under moisture conditions typical of wheat-growing areas of Japan. Thus, Psy-E1 has the potential to contribute high YPC in durum wheat breeding programs, although the applicable cultivation environments are limited.

Barley (Hordeum vulgare) is widely cultivated, ranking fourth in cultivation area among cereal crops worldwide. Many wild and cultivated barley accessions have been collected and preserved in crop genebanks throughout the world. Barley has a large genome (~5 Gbp) that has recently been sequenced and assembled at the chromosome level by the international research community. The community also is sequencing accessions representing the diversity of both domesticated and wild barley to provide genome-wide genotyping information for pangenome analysis. Given that the pangenome represents the universe of genome sequences existing in a species, the long-term goal of this project is to obtain high-quality genome sequences of the major barley accessions worldwide. As each accession is annotated, the capacity to explore structural differences is enhanced by the increased understanding of the diversity of the barley genome, which will facilitate efficient development of cultivars for human consumption. This review describes our current knowledge of barley genome diversity and proposes future directions for basic and applied research of the barley pangenome.

The genus Citrus includes 162 species, but sweet oranges, grapefruits, lemons, and mandarins dominate global trade. For over 100 years, many native citrus cultivars have seen limited production. With the growing demand for new hybrid scions with higher sugar content, easy peeling, and good aroma, minor genetic resources offer potential for breeding, although low selection rates have limited their use. Recent genome sequencing of major citrus cultivars has advanced DNA marker and marker-assisted selection techniques. Additionally, Genome-wide Association Studies have identified key quantitative trait loci, and genomic prediction studies show higher prediction scores for various fruit traits. Genomic studies have clarified the origin and evolution of the genus Citrus, revealing that current species are hybrids of four ancient taxa (C. maxima, C. medica, C. reticulata, and C. micrantha) with several minor taxa, prompting a revision of the classification. Pedigree analysis of 67 native cultivars highlights the potential of some, like Kishu, Tachibana, Kaikoukan, and Kunenbo, as breeding parents. These advances have deepened our understanding of citrus origins, as well as the processes of domestication and diversification, revolutionizing breeding practices and enhancing the use of genetic resources in the citrus breeding program at the National Agriculture and Food Research Organization.