Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

Abstract

BackgroundApparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited.ResultsIn this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers.ConclusionsThe addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx a and Wx b alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.

Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India

“…With the introduction of high yielding and hybrid varieties, though yield has been enhanced, the genetic base of rice cultivars has narrowed down [57,58]. In the present collection of aromatic rices, a moderate population structure was detected as found in North-Eastern [49], a diverse origin [59] and in the North Korean [55] collections. The aromatic rice from Odisha was differentiated into two sub-populations (SP1 and SP2).…”

Generation of targeted mutant rice using a CRISPR‐Cpf1 system

“…Rice is the most frequently used crop species for testing and applying CRISPR‐Cas9 tools. Several agronomic traits of rice, including yield, fertility, architecture, biotic and abiotic stress response, and herbicide tolerance, have been successfully modified by targeted mutations in one or multiple major genes (Ikeda et al ., 2016; Li et al ., 2016a,b,c; Osakabe et al ., 2016; Sun et al ., 2016; Wang et al ., 2016; Xu et al ., 2014, 2016; Zhou et al ., 2015). …”

Field Trials Reveal Ecotype-Specific Responses to Mycorrhizal Inoculation in Rice

“…To meet global needs, a 40% increase in production of rice must be achieved in the next 20 years on limited and increasingly degraded arable lands and in an unstable global climate context [3–4]. Sub-Saharan Africa is largely dependent on rice import for its food security.…”

“…However, the yields are still low [7] and the prohibitive cost and environmental problems caused by chemical inputs [8–10] support the search for new sustainable strategies to promote soil fertility and improve rice production. These approaches include the application of organic fertilizers, the use of nitrogen-fixing green manure ( Azolla sp., fallow legumes) and of beneficial rhizospheric microorganisms such as arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPB) and the selection of root systems for improved water and nutrient acquisition [4]. …”