Genetic diversity analysis reveals importance of Green Revolution Gene (Sd1 Locus) for drought tolerance in rice

57499Authors: Vikram, P.; Kadam, S; Singh, B.P; You Jin lee; Jitendra Kumar Pal; Singh, S; Singh, O.N; Mallikarjuna Swamy, B.P; Thiyagarajan, K; Sukhwinder-Singh; Singh, N.K.

Published in: Agricultural Research, In press.


Genetic diversity analysis based on genome-wide single-nucleotide polymorphism (SNP) assay of a set of Indian rice cultivars including modern high-yielding varieties and landraces revealed two broad groups, one with “Aus” and the other with “Indica” cultivars. Marker analysis of these genotypes was carried out for three major drought tolerance QTLs as well as green revolution gene, sd1. This gene collocates with a drought QTL, qDTY 1.1 . The well-known drought-tolerant landraces or traditional varieties had the “tall” allele of the sd1 gene, indicating the possibility of close linkage, pleiotropy or both associated with this gene. Profiling of rice genotypes investigated in the present study with drought QTL markers, genome-wide SNPs, and sd1 gene reveals the importance of using multiple genes rather focusing on any single major QTL/gene for drought tolerance. Our results suggested that rice genetic improvement for rain-fed areas require enhanced use of pre-green revolution varieties.

Factors preventing the performance of oxygen isotope ratios as indicators of grain yield in maize

57445Authors: Sanchez-Bragado, R.; Araus, J.L; Scheerer, U; Cairns, J.E; Rennenberg, H; Ferrio, J.P.

Published in: Planta, 2016, vol. 243, no.2, p.355-368.


This paper provides new insights into source-sink relationships and transpiration processes which will eventually help to interpret δ 18 O as a genotype selection and ecophysiological tool for maize adaptation to drought.

Oxygen isotope composition (δ18O) has been proposed as a phenotyping tool to integrate leaf transpiration in C4 crops, such as maize. Within this context we hypothesize that δ18O in leaves may reflect primarily environmental and genetic variability in evaporative processes, but that this signal may become dampened in transit from source to sink tissues. The aim of this study was to assess the relative importance of transpirative or translocation-related factors affecting δ18O in plant tissues of maize. We performed two water regime experiments, one with two varieties under semi-controlled conditions, and another in the field with 100 genotypes during two consecutive years. The δ18O in organic matter at the leaf base was strongly correlated with the δ18O in stem water, indicating that it could be a good proxy for source water in extensive samplings. Compared to leaves, we observed an 18O depletion in silks and grains, but not in stem-soluble organic matter. We interpret this as evidence of exchange with unenriched water from source to sink, but mainly occurring within sink tissues. Although grain yield (GY) and physiological variables did not show clear intra-trial patterns against δ18O, the only tissues that correlated with GY in the linear regression approach were that of silks, giving an insight of evapotranspirative demand during female flowering and thus of potential maize lines that are better adapted to drought. This finding will eventually help to interpret δ18O as a genotype selection and ecophysiological tool for the adaption of maize and other crops to drought, offering insight into source-sink relationships and transpiration processes.

Effects of conservation agriculture on crop productivity and water-use efficiency under an irrigated pigeonpea–wheat cropping system in the western Indo-Gangetic Plains

57502Authors: Das, T.K.; Bandyopadhyay, K.K; Bhattacharya, R; Sudhishri, S; Sharma, A.R; Behera, U.K; Saharawat, Y.S; Sahoo, P; Pathak, H; Vyas, A.K; Bhar, L.M; Gupta, H.S; Gupta, R.K; Jat, M.L.

Published in: In: Journal of Agricultural Science In press


In search of a suitable resource conservation technology under pigeonpea (Cajanus cajan L.)–wheat (Triticum aestivum L.) system in the Indo-Gangetic Plains, the effects of conservation agriculture (CA) on crop productivity and water-use efficiency (WUE) were evaluated during a 3-year study. The treatments were: conventional tillage (CT), zero tillage (ZT) with planting on permanent narrow beds (PNB), PNB with residue (PNB + R), ZT with planting on permanent broad beds (PBB) and PBB + R. The PBB + R plots had higher pigeonpea grain yield than the CT plots in all 3 years. However, wheat grain yields under all plots were similar in all years except for PBB + R plots in the second year, which had higher wheat yield than CT plots. The contrast analysis showed that pigeonpea grain yield of CA plots was significantly higher than CT plots in the first year. However, both pigeonpea and wheat grain yields during the last 2 years under CA and CT plots were similar. The PBB + R plots had higher system WUE than the CT plots in the second and third years. Plots under CA had significantly higher WUE and significantly lower water use than CT plots in these years. The PBB + R plots had higher WUE than PNB + R and PNB plots. Also, the PBB plots had higher WUE than PNB in the second and third years, despite similar water use. The interactions of bed width and residue management for all parameters in the second and third years were not significant. Those positive impacts under PBB + R plots over CT plots were perceived to be due to no tillage and significantly higher amount of estimated residue retention. Thus, both PBB and PBB + R technologies would be very useful under a pigeonpea–wheat cropping system in this region.

Agronomic improvements can make future cereal systems in South Asia far more productive and result in a lower environmental footprint

57503Authors: Jagdish Kumar Ladha; Adusumilli Narayana Rao; Raman, A.K; Tirol Padre, A; Dobermann, A; Gathala, M.K; Kumar, V; Saharawat, Y.S; Sharma, S; Piepho, H.P; Md Mursedul Alam; Liak, R; Rajendran, R; Chinnagangannagari Kesava Reddy; Parsad, R; Sharma, P.C; Singh, S.S; Saha, A; Shamsoon Noor.

Published in: Global Change Biology In press

South Asian countries will have to double their food production by 2050 while using resources more efficiently and minimizing environmental problems. Transformative management approaches and technology solutions will be required in the major grain-producing areas that provide the basis for future food and nutrition security. This study was conducted in four locations representing major food production systems of densely populated regions of South Asia. Novel production-scale research platforms were established to assess and optimize three futuristic cropping systems and management scenarios (S2, S3, S4) in comparison with current management (S1). With best agronomic management practices (BMPs), including conservation agriculture (CA) and cropping system diversification, the productivity of rice- and wheat-based cropping systems of South Asia increased substantially, whereas the global warming potential intensity (GWPi) decreased. Positive economic returns and less use of water, labor, nitrogen, and fossil fuel energy per unit food produced were achieved. In comparison with S1, S4, in which BMPs, CA and crop diversification were implemented in the most integrated manner, achieved 54% higher grain energy yield with a 104% increase in economic returns, 35% lower total water input, and a 43% lower GWPi. Conservation agriculture practices were most suitable for intensifying as well as diversifying wheat–rice rotations, but less so for rice–rice systems. This finding also highlights the need for characterizing areas suitable for CA and subsequent technology targeting. A comprehensive baseline dataset generated in this study will allow the prediction of extending benefits to a larger scale.

Linkage analysis and map construction in genetic populations of clonal F1 and double cross

56923Authors: Luyan Zhang; Huihui Li; Jiankang Wang

Published in: G3, 2015, vol. 5


In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that allow the estimation of female, male, and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified and another five scenarios are present for recombination frequency estimation.

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Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross

56921Authors: Luyan Zhang; Huihui Li; Junqiang Ding; Jianyu Wu; Jiankang Wang.

Published in: Journal of integrative plant biology, In press

In this study, we considered five categories of molecular markers in clonal F1 and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F1 and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in Inclusive Composite Interval Mapping (ICIM) of QTL. The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple-QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.

Chapter 17: Biometrical approaches for analysis of phenotypic data of complex traits

56919Authors: Huihui Li; Jiankang Wang

Published in the book: Phenomics in crop plants: trends, options and limitations.

Phenotype (or phenotypic value) is the performance of a trait in interest, which can be observed in the field and then used in estimating the unknown genotypic value (or the phenotypic mean). In this chapter, we introduced statistical approaches to analyze three types of phenotypic observation, i.e., (1) replicated observations of one genotype in one environment, (2) replicated observations of multiple genotypes in one environment, and (3) replicated observations of multiple genotypes in multiple environments. The principle of analysis of variance (ANOVA) was applied on each kind of phenotypic data. From the results of ANOVA, we can further estimate genotypic value, genetic effects, variance components, heritability, etc., which can be further used in genetic studies and breeding applications. In the end, we present a computer tool implemented in the integrated genetic software QTL IciMapping, which includes the biometrical approaches introduced in this chapter and can be readily used in phenotyping complex traits.

Genetic dissection on rice grain shape by the two-dimensional image analysis in one japonica × indica population consisting of recombinant inbred lines

56918Authors: Yin, C.; Huihui Li; Li, S; Xu, L; Jiankang Wang; Zhigan Zhao.

Published in: Theoretical and Applied Genetics, In press

Two-dimensional (2D) digital image analysis is efficient for investigating the rice grain shape characters in large genetic and breeding populations. In this study, we used 2D image analysis to investigate seven characters, i.e., grain length (GL), grain width (GW), length-to-width ratio (LW), grain area (GA), grain circumference (GC), grain diameter (GD), and grain roundness (GR), in one japonica × indica genetic population consisting of 215 recombinant inbred lines. GL and GW can be recorded manually as well, and have been extensively used together with LW (i.e., GL/GW) in genetic studies on grain shape. GC and GA can be hardly measured manually, and have not been used together with GD and GR. Results indicated that the seven characters could be precisely measured by 2D image analysis, genotype by environment interaction was low, and heritability was high. Each character was controlled by a few major stable genes and multiple minor additive genes. A total of 51 QTL were detected for the seven characters across four diverse environments, 22 from GL, GW, and LW, the three traditional characters, and 29 from the other four characters. The 51 QTL were clustered in eighteen marker intervals. Comparing with previous studies and analyzing the stability of identified QTL, we found six non-reported marker intervals, one each on chromosomes 2 and 3, and two each on chromosomes 6 and 8. The newly identified loci and the large-scale phenotyping system would greatly improve our knowledge about the genetic architecture and the future rice breeding on grain shape.

Using the UK reference population Avalon X Cadenza as a platform to compare breeding strategies in elite Western European bread wheat

56917Authors: Ma, J., Wingen, L.U; Orford, S; Fenwick, P; Jiankang Wang; Griffiths, S.

Published in: Molecular Breeding, 2015, vol. 35, p. 70

Wheat breeders select for qualitative and quantitative traits, the latter often detected as quantitative trait loci (QTL). It is, however, a long procedure from QTL discovery to the successful introduction of favourable alleles into new elite varieties and finally into farmers’ crops. As a proof of principle for this process, QTL for grain yield (GY), yield components, plant height (PH), ear emergence (EM), solid stem (SS) and yellow rust resistance (Yr) were identified in segregating UK bread wheat reference population, Avalon 9 Cadenza. Among the 163 detected QTL were several not reported before: 17 for GY, the major GYQTL on 2D; a major SS QTL on 3B; and Yr6 on 7B. Common QTL were identified on ten chromosomes, most interestingly, grain number (GN) was found to be associated with Rht-D1b; and GY and GN with a potential new allele of Rht8. The interaction of other QTL with GY and yield components was discussed in the context of designing a UK breeding target genotype. Desirable characteristics would be: similar PH
and EM to Avalon; Rht-D1b and Vrn-A1b alleles; high TGW and GN; long and wide grains; a large root system, resistance to diseases; and maximum GY. The potential of the identified QTL maximising transgressive segregation to produce a high-yielding and resilient genotype was demonstrated by simulation. Moreover, simulating breeding strategies with F2 enrichment revealed that the F2–DH procedure was superior to the RIL and the modified SSD procedure to achieve that genotype. The proposed strategies of parent selection and breeding methodology can be used as guidance for marker-assisted wheat breeding.

Where to target Conservation Agriculture for African smallholders? How to Overcome Challenges Associated with its Implementation? experience from Eastern and Southern Africa

56915Author: Baudron, F.; Thierfelder, C.; Nyagumbo, I.; Gerard, B.

Published in: Environments, 2015, vol. 2, p. 338–357


Since the paper by Giller et al. (2009), the debate surrounding the suitability of conservation agriculture (CA) for African smallholders has remained polarized between proponents and opponents. The debate also gave rise to a few studies that attempted to identify the “niche” where CA would fit in the region, but the insight offered by these studies has been limited. In this paper, we first analyze the rationale of adoption where it occurred globally to define “drivers” of adoption. Our analysis suggests that CA has first and foremost been adopted under the premises of being energy-saving (time and/or power), erosion-controlling, and water-use efficient, but rarely to increase yield. We then define the niche where CA fits, based on these drivers of adoption, as systems where (1) the energy available for crop establishment is limited and/or costly (including labor and draft power); (2) delayed planting results in a significant yield decline; (3) yield is limited or co-limited by water; and/or (4) severe erosion problems threaten the short- to medium-term productivity of farmland. In Eastern and Southern Africa, this niche appears rather large and likely to expand in the near future. When implemented within this niche, CA may still be limited by “performance challenges” that do not constitute drivers or barriers to adoption, but limitations to the performance of CA. We argue that most of these performance challenges can (and should) be addressed by agronomic and socio-economic research, and provide four examples where the International Maize and Wheat Improvement Center (CIMMYT) and its partners have been successfully alleviating four very different challenges through research and development (R&D) in Eastern and Southern Africa. Finally, we describe an iterative and multi-scale R&D approach currently used by CIMMYT in Eastern and Southern Africa to overcome challenges associated with the implementation of CA by African smallholders. This approach could also be useful for other complex combinations of technologies aiming at sustainable intensification.