Nitrogen (N) is a major input cost in rice production, in addition to causing severe pollution to agricultural and ecological environments. Root dry weight has been considered the most important component related to crop yields than the other root traits. Therefore, development of rice varieties/lines with low input of N fertilizer and higher root traits are essential for sustainable rice production. In this context, a main effect quantitative trait locus qRDWN6XB on the long arm of chromosome 6 which positively confers tolerance to N deficiency in the Indica rice variety XieqingzaoB, was identified using a chromosomal segment substitution line (CSSL) population. qRDWN6XB was determined to be located near marker InD90 on chromosome 6 based on association analysis of phenotype data from three N levels and 120 polymorphic molecular markers. The target chromosomal segment substitution line CSSL45, which has the higher root dry weight (RDW) than indica cultivar Zhonghui9308 and carry qRDWN6XB, was selected for further study. A BC5F2:3 population derived from a cross between CSSL45 and Zhonghui9308 was constructed. To fine-map qRDWN6XB, we used the homozygous recombinant plants and ultimately this locus was narrowed to a 52.3-kb between markers ND-4 and RM19771, which contains nine candidate genes in this region. One of these genes, LOC_Os06g15910 as a potassium transporter was considered a strong candidate gene for the RDWN6XB locus. The identification of qRDWN6XB provides a new genetic resource for breeding rice varieties and a starting point to improve grain yield despite the decreased input of N fertilizers. The newly developed and tightly linked InDel marker ND-4 will be useful to improve the root system architecture under low N by marker-assisted selection (MAS) in rice breeding programs.

Heading date (HD) is one of the agronomic traits that influence maturity, regional adaptability, and grain yield. The present study was a follow-up of a previous quantitative trait loci (QTL) mapping study conducted on three populations, which uncovered a total of 62 QTLs associated with 10 agronomic traits. Two of the QTLs for HD on chromosome 7 (qHD7a and qHD7b) had a common flanking marker (RM3670) that may be due to tight linkage, and/or weakness of the statistical method. The objectives of the present study were to map QTLs associated with HD in a set of 76 chromosome segment substitution lines (CSSLs), fine map and validate one of the QTLs (qHD7b) using 2997 BC₅F_2:3 plants, and identify candidate genes using sequencing and expression analysis. Using the CSSLs genotyped with 120 markers and evaluated under two short-day and two long-day growing conditions, we uncovered a total of fourteen QTLs (qHD2a, qHD4a, qHD4b, qHD5a, qHD6a, qHD6b, qHD7b, qHD7c, qHD8a, qHD10a, qHD10b, qHD11a, qHD12a, and qHD12b). However, only qHD6a and qHD7b were consistently detected in all four environments. The phenotypic variance explained by qHD6a and qHD7b varied from 10.1% to 36.1% (mean 23.1%) and from 8.1% to 32.8% (mean 20.5%), respectively. One of the CSSL lines (CSSL52), which harbored a segment from the early heading XieqingzaoB (XQZB) parent at the qHD7b locus, was then used to develop a BC₅F_2:3 population for fine mapping and validation. Using a backcross population evaluated for four seasons under different day lengths and temperatures, the qHD7b interval was delimited to a 912.7-kb region, which is located between RM5436 and RM5499. Sequencing and expression analysis revealed a total of 29 candidate genes, of which Ghd7 (Os07g0261200) is a well-known gene that affects heading date, plant height, and grain yield in rice. The ghd7 mutants generated through CRISPR/Cas9 gene editing exhibited early heading. Taken together, the results from both the previous and present study revealed a consistent QTL for heading date on chromosome 7, which coincided not only with the physical position of a known gene, but also with two major effect QTLs that controlled the stigma exertion rate and the number of spikelets in rice. The results provide contributions to the broader adaptability of marker-assisted breeding to develop high-yield rice varieties.

Summary: Line × Tester experiment was carried out at the Experimental Farm of Rice Research and Training Center (RRTC), Sakha, Kafrelsheikh, Egypt during three growing seasons to evaluate the performance of 21 F1 hybrids along with their parents. Three cytoplasmic male sterile lines, two wild abortive (Wild Abortive); IR69625A, IR70368A and one (Kalinga) K17A as female were tested with seven cultivars/lines as testers. The analysis of variance detected that, highly significant variations among genotypes (parental lines with their crosses) for all traits in both seasons and in their combined analysis. Two hybrid combinations; IR69625A×Giza178 and IR69625A×Giza179 were recorded the best values for grain yield under both seasons and their combined. General combining ability (GCA) and specific combining ability (SCA) effects of genotypes for the studied traits were estimated. The results indicated that, K17A (female) and Giza 179 (male) were the best combiner for early heading date and could be useful to breed early maturing rice cultivars. The CMS line IR69625A and Giza178, Giza179 gave highly significant and positive GCA value and so appeared to be good parental lines combiner in hybrid combinations for high grain yield/plant. The positive values of GCA mean increased for grain yield/plant, which could be useful in breeding programs for high yield potential rice cultivars. The hybrid combination IR69625A×Giza179 showed highly significant and positive SCA estimates under both seasons and their combined. In conclusion, it is clear that this hybrid seemed promising hybrid for earliness and high grain yield under Egyptian conditions.

The exploitation of hybrid rice technology has been made possible by the identification of restorers and maintainers as parental lines. Four CMS lines of rice viz., E2015A, G46A, CCG5A, and E0034A were crossed with 24 diverse testers during the growing seasons of 2022 in Experimental Farm of RRTC, Sakha, Egypt. Ninety-six hybrid combinations were generated to identify the effective restores and maintainers from elite local and exotic rice genotypes under test cross nursery and determine the best heterotic combinations in terms of yield and its components during 2023 seasons. The F1 hybrids expressed different fertility reactions. Out of 96 test crosses the results of this investigation revealed that sixteen rice genotypes of tested 24 rice parents were identified as effective restorers (R) which can easily restore four different sources of CMS lines (Pollen fertility and spikelet fertility more than 83%) with heterotic morphological attributes. On the contrary, three rice genotypes of 24 rice parents (BN-19, BN-45, and Winixyan) were identified as maintainers (M) for the same aforementioned CMS lines. Among the fourteen F1 hybrids, assessment of standard heterosis based on the standard check (Giza 178) of five effectively restored cross combinations showed higher useful heterosis than the standard check variety. Three hybrid combinations i.e. E0034A/SR-86 (26.41%) and E0034A/GZ10848 (25.51%) recorded more than 25% yield advantage over the check variety Giza 178. Restorers and maintainers identified illustrate the possibility of the development of new rice hybrids and CMS lines in the future.